Gamescope is even fully open-source, so you could remove the steam deck UI, and still run any game with the same performance benefits of not running it inside KDE. Of course also, you could flash a new OS on the device itself if you wanted to entirely remove Valve’s presence.
Changes get wiped because (as you mentioned) it's an a/b partition; when you switch partitions you lose the changes.
You can actually enable an overlay for root changes, but this causes other issues - you get to choose if you want to track packages you've installed, or packages that are in the base system. It's either in the overlay and you keep your changes but not the base system changes, or it's in the base system and you lose track of changes made in your overlay. - updates to the base system of packages that have been uninstalled in the overlay can cause inconsistencies like orphaned files (the new system update includes extra files from this package that haven't been removed by your uninstall. Hopefully some other package doesn't take this as a sign that an optional dependency library is fully installed, the linked subdependencies might be missing) - updates to the base system can be overridden in specific files that were modified in your overlay, causing packages to become non-functional - imagine rebuilding a library 4.5 to add a feature (or updating to v 4.7), then the base system updates that library to 4.8. All other software now expects version 4.8, but instead your overlay is providing 4.5. better hope it's only a minor patch update and not an update providing a feature, or worse, a major breaking update.
