Inter process messaging seems to be have quite some attention right now. I don't think it's very far now, if KeepassXC/Firefox issue I'm following is any indication.
When two flatpacks package the same library, they duplicate memory use.
I've been running fairly low ram machines and I genuinely haven't noticed any difference. Maybe I haven't run enough of them at the same time and them having different (not shared) libraries. I wonder what the benchmarks are on this. I've only seen threads where people say it uses a bit more but no real comparison.
end-all, be-all package format.
I'm not sure if that's the direction. I think flatpak is specifically targeting GUI apps, with the "system" packages being traditional packages. And I think that's a good solution, that way you'd have a tighter system layer that could even be immutable and you'd have a separate application layer, so they don't mess with each other. Good for preventing breakage of the system if there's somehing fucky with some app.