The nice thing about atomic distros is switching operating systems is as easy as typing 'ostree rebase', and registering a secure boot key.
So if Bazzite did go that way you could have fedora running in under an hour and with flatpak most thing will just work.
As I understand 'ostree rebase' between KDE and Gnome will lead to broken system.
I want to bear witness that I did exactly that when I downmoted one of my computers from 'gaming machine' to 'closet server'.
One `rpm-ostree rebase` from Bazzite to a server-oriented flavour of Fedora Silverblue and it's been running and updating flawlessly since then.