Starting with Linux kernel version 5.13 podman can use a native overlay filesystem instead of relying on fuse-overlayfs which has significant performance improvements.
According to https://www.redhat.com/sysadmin/podman-rootless-overlay it does require running podman system reset to reset some metadata. Because VyOS does not support user data volumes, and requires binding to a source directory, I don't think we need to worry about data migration.
There are some notes of archlinux switching to kernel overlay in https://bugs.archlinux.org/task/71358
The VyOS path for the .has-mount-program file is:
/usr/lib/live/mount/persistence/container/storage/overlay/.has-mount-program