Flatpak is basically running an isolated separate distro. A software inside a Flatpak has to communicate with the outside world to do anything useful which is yet another API surface that needs to be maintained and it will be dropped just like gtk2 when people just don't want to maintain it.

I think the way the Linux ecosystem works is fundamentally against maintaining old binaries unless they are a text-only program.

Not an expert but i don't see a problem. I use Snap-packaged compilers on Ubuntu all day, and have used Flatpak'd IDEs