Me again from the other thread.
Have a look at this and think about whether it sounds familiar: "sudo podman system reset" deletes current working directory · Issue #18349 · containers/podman · GitHub
There have been multiple bugs with older versions of podman where it will pick up a CWD inappropriately, or in some cases, even cache it in per-user or system-wide state to continue to be used inappropriately (in one case mentioned in the bug report, an old and very wrong path continued to be used even after fixes were applied as it was in the libpod cache).
That you’re seeing a lot of overlays appear in the homedirs sounds somewhat similar to me - that’s the place you’d most likely be running podman from. It’s possible that you’ve either manually run it from /config as well, or internal VyOS machinery using /config as a CWD has executed podman commands.
That it’s appeared and become a lot more frequent all of a sudden would also lend itself towards bad state being cached somewhere.
I don’t have a direct suggestion on how to solve it though, beyond updating to the latest VyOS (which includes a very recent podman) and resetting as much of the podman state as possible.