As someone not as involved, it's hard to follow why it's a mess.
The actual installation with flatpak also seems to use
flatpak install --user flathub-beta org.gimp.GIMP
and the make current is only for managing the active installation. From someone that has never used flatpak it doesn't seem more a mess than apt or the deb way in any way and also manages to have the unstable and stable version installed at the same time (which apt doesn't as far as I remember).
Am I missing some hidden problem besides that it's not available in the manager of choice?