all changes in etc are snapshotted with each update so you could just roll back to your previous version and it would fix it.
I assume you meant you messed up permissions in your home directory, and yes that is pretty much the only place you can permanently mess something up with silverblue.
With fedora atomic, lets say i wanted to try out kde desktop for a while. i would first pin my current build so i can roll back to it if i dont end liking kde with
Then i would rebase to the kde branch with
Then just reboot. That’s literally it and i would have a kde system with all my layered packages and i could roll back to my old system at anytime.