They do talk about how the library deduplication in memory is an OS feature and nothing to do with flatpak so it's possible that the same library being shared might be dedupped whether it is in same runtime or not. But I don't know. In any case, I guess extra RAM use is possible but I don't think (from personal experience and reading up on it) that it's very noticeable. Not to mention a lot of the used libraries do come with the runtimes, so that alleviates the issue if the dedupping isn't happening.

Whereas about how much of the system goes in flatpacks, once you've put your DE and apps on it, that's like 80% of a typical desktop software load. There's not much left and, like you said, the rest can be immutable. You may argue the DE is part of the base system, and I'd agree with you, but many people don't.

I think the intention is to keep at least some parts of the DE outside of it, but the apps that make it as flatpaks. So for KDE I think it would be something like the shell, file indexer, "low level" stuff like that out and image viewer, media player, browser, "apps" like that in flatpaks. Which does break the DE up but makes sense to me, with "system" being separated from "apps".

Veering off topic for a bit... TBH it feels a little too much like Windows for my taste. When apps have a package maintainer, you can choose the level of stability you want and developers can focus on adding features / optimizing. When you remove that layer, the developers need to figure out how stable to keep their app to cater to most users, and if you are not comfortable with that, tough luck.

You could have "stable repos" for flatpaks, maintained by distros but I feel like it would take away some of the point of it (being to ease distro repo maintainer workload). Some devs will be happy that there's no "meddling" distro maintainers, which is a complaint I've sometimes seen from devs. I think the idea that the apps come straight from the devs is both good and bad. Good in that it's how the dev intended and updates are possible much quicker. Bad in that often the modification distros do serve a good purpose, of making the app better fit in to the whole or fixing stuff that misbehabes but for whatever reason hasn't been fixed upstream.