This is pretty much what I noted in your previous thread. It’s just the way that ostree works. It’s not corruption.
If you want to use custom binaries and libs like wine you will want to maintain them entirely under /home.
So: use your home directory, not /mnt.
ostree does not exactly use snapshots but something more like “hardlink farms from an object database”, which means that the disk space required is generally much less than what you would expect. Also, the current ostree and the previous one is kept, but others are automatically cleaned up. So there isn’t normally a need for the user to worry about purging old versions etc. But if you’d like to poke at this as an expert, you can check the docs under man ostree-admin, man ostree and the additional pages referenced there.