Disclaimer: I understand that it is explicitly stated not to do this, but…
Is it possible? If so, what issues can I expect? I manage all my programs in all the recommended ways. I’ve installed no extensions or themes. It really might as well be out of the box except for a handful of files in the user space.
The biggest issues you may run into is theming, as well as the wallet not working properly. For theming, some apps may behave wierdly since there are many different themes (gtk3, gtk 4, qt, etc) and the transfer isnt always perfect.
For the wallet, some apps may complain that you need to enter your password, or you may need to relogin. This is because Gnome and KDE use different managers (wallets) to manage logins and there can be issues switching between them.
Then lastly, as you mentioned, there may be some config drift. Even you haven’t changed all that much, Gnome may have put certain settings in place. KDE may not overwrite them and you might get some wierdness here and there. The theming issues are an example, but there may other stuff like default apps.
Overall it isn’t the worst thing in the world to do, but if you do it, just know that there may be wierd stuff going on. Sometimes you may encounter a bug and it will be difficult to say if the software you’re using is the issue, or if switching desktops is the issue. One other thing you could possibly do is have a seperate user just for bazzite and migrate ay user data you consider important. If you ever want to return to bazzite-gnome, just use the current user again.