Can't set graphRoot and runRoot via configuration

Issue Description

Hello. I'm currently developing completely portable rootless distrobox/podman installation for using ALVR under Linux and have discovered some issues with setting configuration for storage.conf. So to make it completely portable (so that it never interferes with other configurations) i need to override pretty much every single configuration that is related to containers, volumes, etc etc, and that includes graphRoot and runRoot. When i tried doing so, it still pointed at home folder and same xdg runtime directory.

Steps to reproduce the issue

Steps to reproduce the issue

1. Install rootless podman onto user
2. Change runroot and graphroot in storage.conf
3. run podman info

Describe the results you received

Graphroot and runroot points to same location

Describe the results you expected

Graphroot and runroot should point to location i've specified in storage.conf

podman info output

host:
  arch: amd64
  buildahVersion: 1.30.0
  cgroupControllers:
  - cpu
  - io
  - memory
  - pids
  cgroupManager: systemd
  cgroupVersion: v2
  conmon:
    package: Unknown
    path: /home/plyshka/Documents/Code/Containers/alvr-distrobox/tmp-test/podman/lib/podman/conmon
    version: 'conmon version 2.1.7, commit: f633919178f6c8ee4fb41b848a056ec33f8d707d'
  cpuUtilization:
    idlePercent: 98.62
    systemPercent: 0.33
    userPercent: 1.04
  cpus: 12
  databaseBackend: boltdb
  distribution:
    distribution: fedora
    variant: silverblue
    version: "38"
  eventLogger: file
  hostname: plyshka
  idMappings:
    gidmap:
    - container_id: 0
      host_id: 1000
      size: 1
    - container_id: 1
      host_id: 100000
      size: 65536
    - container_id: 65537
      host_id: 260000
      size: 65537
    uidmap:
    - container_id: 0
      host_id: 1000
      size: 1
    - container_id: 1
      host_id: 100000
      size: 65536
    - container_id: 65537
      host_id: 260000
      size: 65537
  kernel: 6.2.11-300.fc38.x86_64
  linkmode: dynamic
  logDriver: k8s-file
  memFree: 17411289088
  memTotal: 33557540864
  networkBackend: cni
  ociRuntime:
    name: crun
    package: Unknown
    path: /home/plyshka/Documents/Code/Containers/alvr-distrobox/tmp-test/podman/bin/crun
    version: |-
      crun version 1.8.4
      commit: 5a8fa99a5e41facba2eda4af12fa26313918805b
      rundir: /run/user/1000/crun
      spec: 1.0.0
      +SYSTEMD +SELINUX +APPARMOR +CAP +SECCOMP +EBPF +CRIU +YAJL
  os: linux
  remoteSocket:
    path: /run/user/1000/podman/podman.sock
  security:
    apparmorEnabled: false
    capabilities: CAP_CHOWN,CAP_DAC_OVERRIDE,CAP_FOWNER,CAP_FSETID,CAP_KILL,CAP_NET_BIND_SERVICE,CAP_SETFCAP,CAP_SETGID,CAP_SETPCAP,CAP_SETUID,CAP_SYS_CHROOT
    rootless: true
    seccompEnabled: true
    seccompProfilePath: /usr/share/containers/seccomp.json
    selinuxEnabled: true
  serviceIsRemote: false
  slirp4netns:
    executable: /home/plyshka/Documents/Code/Containers/alvr-distrobox/tmp-test/podman/bin/slirp4netns
    package: Unknown
    version: |-
      slirp4netns version 1.2.0
      commit: 656041d45cfca7a4176f6b7eed9e4fe6c11e8383
      libslirp: 4.7.0
      SLIRP_CONFIG_VERSION_MAX: 4
      libseccomp: 2.5.4
  swapFree: 8589930496
  swapTotal: 8589930496
  uptime: 2h 52m 59.00s (Approximately 0.08 days)
plugins:
  authorization: null
  log:
  - k8s-file
  - none
  - passthrough
  network:
  - bridge
  - macvlan
  - ipvlan
  volume:
  - local
registries:
  search:
  - docker.io
  - registry.fedoraproject.org
  - registry.access.redhat.com
store:
  configFile: /home/plyshka/Documents/Code/Containers/alvr-distrobox/tmp-test/.config/containers/storage.conf
  containerStore:
    number: 0
    paused: 0
    running: 0
    stopped: 0
  graphDriverName: overlay
  graphOptions:
    overlay.ignore_chown_errors: "true"
    overlay.mount_program:
      Executable: /home/plyshka/Documents/Code/Containers/alvr-distrobox/tmp-test/podman/bin/fuse-overlayfs
      Package: Unknown
      Version: |-
        fuse-overlayfs: version 1.11
        fusermount3 version: 3.13.1
        FUSE library version 3.14.1
        using FUSE kernel interface version 7.31
    overlay.mountopt: nodev,fsync=0
  graphRoot: /var/home/plyshka/.local/share/containers/storage
  graphRootAllocated: 998483427328
  graphRootUsed: 769376677888
  graphStatus:
    Backing Filesystem: btrfs
    Native Overlay Diff: "false"
    Supports d_type: "true"
    Using metacopy: "false"
  imageCopyTmpDir: /var/tmp
  imageStore:
    number: 0
  runRoot: /run/user/1000/containers
  transientStore: false
  volumePath: /home/plyshka/Documents/Code/Containers/alvr-distrobox/tmp-test/.local/share/containers/volume
version:
  APIVersion: 4.5.0
  Built: 0
  BuiltTime: Thu Jan  1 05:00:00 1970
  GitCommit: ""
  GoVersion: go1.18.10
  Os: linux
  OsArch: linux/amd64
  Version: 4.5.0

Podman in a container

No

Privileged Or Rootless

Rootless

Upstream Latest Release

Yes

Additional environment details

Running on Fedora Silverblue 38, installing podman using this script

Additional information

storage.conf

# See https://github.com/containers/storage/blob/master/docs/containers-storage.conf.5.md
# and https://github.com/containers/storage/blob/master/storage.conf
# This file is is the configuration file for all tools
# that use the containers/storage library.
# See man 5 containers-storage.conf for more information
# The "container storage" table contains all of the server options.
[storage]

# Default Storage Driver, Must be set for proper operation.
driver = "overlay"

# Temporary storage location
runroot = "/run/user/1000/distrobox/containers"

# Primary Read/Write location of container storage
graphroot = "/home/plyshka/Documents/Code/Containers/alvr-distrobox/tmp-test/.local/share/containers"

# Storage path for rootless users
#
# rootless_storage_path = "$HOME/.local/share/containers/storage"

[storage.options]
# Storage options to be passed to underlying storage drivers

# AdditionalImageStores is used to pass paths to additional Read/Only image stores
# Must be comma separated list.
additionalimagestores = [
]

# Remap-UIDs/GIDs is the mapping from UIDs/GIDs as they should appear inside of
# a container, to the UIDs/GIDs as they should appear outside of the container,
# and the length of the range of UIDs/GIDs.  Additional mapped sets can be
# listed and will be heeded by libraries, but there are limits to the number of
# mappings which the kernel will allow when you later attempt to run a
# container.
#
# remap-uids = 0:1668442479:65536
# remap-gids = 0:1668442479:65536

# Remap-User/Group is a user name which can be used to look up one or more UID/GID
# ranges in the /etc/subuid or /etc/subgid file.  Mappings are set up starting
# with an in-container ID of 0 and then a host-level ID taken from the lowest
# range that matches the specified name, and using the length of that range.
# Additional ranges are then assigned, using the ranges which specify the
# lowest host-level IDs first, to the lowest not-yet-mapped in-container ID,
# until all of the entries have been used for maps.
#
# remap-user = "containers"
# remap-group = "containers"

# Root-auto-userns-user is a user name which can be used to look up one or more UID/GID
# ranges in the /etc/subuid and /etc/subgid file.  These ranges will be partitioned
# to containers configured to create automatically a user namespace.  Containers
# configured to automatically create a user namespace can still overlap with containers
# having an explicit mapping set.
# This setting is ignored when running as rootless.
# root-auto-userns-user = "storage"
#
# Auto-userns-min-size is the minimum size for a user namespace created automatically.
# auto-userns-min-size=1024
#
# Auto-userns-max-size is the minimum size for a user namespace created automatically.
# auto-userns-max-size=65536

[storage.options.overlay]
# ignore_chown_errors can be set to allow a non privileged user running with
# a single UID within a user namespace to run containers. The user can pull
# and use any image even those with multiple uids.  Note multiple UIDs will be
# squashed down to the default uid in the container.  These images will have no
# separation between the users in the container. Only supported for the overlay
# and vfs drivers.
ignore_chown_errors = "true"

# Path to an helper program to use for mounting the file system instead of mounting it
# directly.
mount_program = "/home/plyshka/Documents/Code/Containers/alvr-distrobox/tmp-test/podman/bin/fuse-overlayfs"

# mountopt specifies comma separated list of extra mount options
mountopt = "nodev,fsync=0"

# Set to skip a PRIVATE bind mount on the storage home directory.
# skip_mount_home = "false"

# Size is used to set a maximum size of the container image.
# size = ""

# ForceMask specifies the permissions mask that is used for new files and
# directories.
#
# The values "shared" and "private" are accepted.
# Octal permission masks are also accepted.
#
#  "": No value specified.
#     All files/directories, get set with the permissions identified within the
#     image.
#  "private": it is equivalent to 0700.
#     All files/directories get set with 0700 permissions.  The owner has rwx
#     access to the files. No other users on the system can access the files.
#     This setting could be used with networked based homedirs.
#  "shared": it is equivalent to 0755.
#     The owner has rwx access to the files and everyone else can read, access
#     and execute them. This setting is useful for sharing containers storage
#     with other users.  For instance have a storage owned by root but shared
#     to rootless users as an additional store.
#     NOTE:  All files within the image are made readable and executable by any
#     user on the system. Even /etc/shadow within your image is now readable by
#     any user.
#
#   OCTAL: Users can experiment with other OCTAL Permissions.
#
#  Note: The force_mask Flag is an experimental feature, it could change in the
#  future.  When "force_mask" is set the original permission mask is stored in
#  the "user.containers.override_stat" xattr and the "mount_program" option must
#  be specified. Mount programs like "/usr/bin/fuse-overlayfs" present the
#  extended attribute permissions to processes within containers rather then the
#  "force_mask"  permissions.
#
# force_mask = ""

[storage.options.thinpool]
# Storage Options for thinpool

# autoextend_percent determines the amount by which pool needs to be
# grown. This is specified in terms of % of pool size. So a value of 20 means
# that when threshold is hit, pool will be grown by 20% of existing
# pool size.
# autoextend_percent = "20"

# autoextend_threshold determines the pool extension threshold in terms
# of percentage of pool size. For example, if threshold is 60, that means when
# pool is 60% full, threshold has been hit.
# autoextend_threshold = "80"

# basesize specifies the size to use when creating the base device, which
# limits the size of images and containers.
# basesize = "10G"

# blocksize specifies a custom blocksize to use for the thin pool.
# blocksize="64k"

# directlvm_device specifies a custom block storage device to use for the
# thin pool. Required if you setup devicemapper.
# directlvm_device = ""

# directlvm_device_force wipes device even if device already has a filesystem.
# directlvm_device_force = "True"

# fs specifies the filesystem type to use for the base device.
# fs="xfs"

# log_level sets the log level of devicemapper.
# 0: LogLevelSuppress 0 (Default)
# 2: LogLevelFatal
# 3: LogLevelErr
# 4: LogLevelWarn
# 5: LogLevelNotice
# 6: LogLevelInfo
# 7: LogLevelDebug
# log_level = "7"

# min_free_space specifies the min free space percent in a thin pool require for
# new device creation to succeed. Valid values are from 0% - 99%.
# Value 0% disables
# min_free_space = "10%"

# mkfsarg specifies extra mkfs arguments to be used when creating the base
# device.
# mkfsarg = ""

# metadata_size is used to set the `pvcreate --metadatasize` options when
# creating thin devices. Default is 128k
# metadata_size = ""

# Size is used to set a maximum size of the container image.
# size = ""

# use_deferred_removal marks devicemapper block device for deferred removal.
# If the thinpool is in use when the driver attempts to remove it, the driver
# tells the kernel to remove it as soon as possible. Note this does not free
# up the disk space, use deferred deletion to fully remove the thinpool.
# use_deferred_removal = "True"

# use_deferred_deletion marks thinpool device for deferred deletion.
# If the device is busy when the driver attempts to delete it, the driver
# will attempt to delete device every 30 seconds until successful.
# If the program using the driver exits, the driver will continue attempting
# to cleanup the next time the driver is used. Deferred deletion permanently
# deletes the device and all data stored in device will be lost.
# use_deferred_deletion = "True"

# xfs_nospace_max_retries specifies the maximum number of retries XFS should
# attempt to complete IO when ENOSPC (no space) error is returned by
# underlying storage device.
# xfs_nospace_max_retries = "0"