Some additions:
* tested a live iso - gnome-classic works just fine
* tested gdm3 - really cool, gdm3 start wayland by default, but gnome-classic seems not to work with wayland - indeed, it doesn't surprise me much - you might ask in #debian-gnome about
* gdm3 has a config option which disable wayland - so xorg should be used - that doesn't work, at least not in a kvm virtual machine - might be the opengl thing - one might ask in #debian-gnome
* sddm and lightdm and i guess even slim should start X+the choosen gnome-session fine - and again - if one encounter problems with, not our problem, we won't change a bit in our setup - take it or not, not really our problem
Same for flatpak -learn to handle it, in case there are bugs - not our problem. I tested it several times and it work just fine - ok, correction, it work as fine as flatpak can work fine - thats a difference
If flatpaks should not be limited to the user (did i mention the --user switch?) it might be that the policykit integration must be installed by the admin of the system. Thats a design decision the flatpak maintainers did intentionally i would guess - so if one don't agree - talk with the flatpak maintainers about or write a bug.
Final note: Damn, i was really surprised and highly excited about the status of wayland in combination with gnome and gdm3 - they did a really awesome job with. One might see this different - but again: not our problem, not our business. In fact - it would be a shame to let go a gnome what is in that good shape.