Wayland is one huge reason why we aren't even calling this "beta". Wayland is absolutely part of the plan. We are working on integration now.
Flatpaks: probably not. Different vision. Flatpak is an 'appstore' type model, not sure we will want that in Subgraph OS, but it's worth a deeper investigation than the thought I've given it so far. There are things in Flatpak that we can benefit from, such as the UI advantages of "Portals". We'll probably be adding support for it to Oz.
I doubt you should even bother with snaps. They don't seem to be that well supported outside of Ubuntu, and I doubt they will ever be.
Therefore Subgraph OS isn't in the worst possible x11 situation, which is the default for every desktop Linux except I think the most recently released Fedora.
Re: iso / updates, we have rolling updates. Installed users are kept current if they install the OS and regularly apply updates and do dist-upgrades.
Also, shouldn't you just use Wayland for the stable 1.0 release? Why even bother with X11 at this point?
Do you plan to support flatpaks as well?