My personal rule of thumb is that if it interacts with the OS or filesystem deeply, native is probably better. E.g. IDEs, cli programs, browsers, Steam etc.

Apps that do a simple things are likely to work perfectly fine on flatpak.

But the problem is that there are outliers in each case. You should pick one and be ready to switch if things don’t work properly.

I seem to remember many random projects joining the foundation. Is this fine? Wouldn’t they dilute their capability to manage a whole bunch of unrelated projects?

Dude, OP is looking for a distro to CONTRIBUTE to because he wants to make year of linux desktop a reality. I think he can use CLI just fine. Looking at how stupid people are these days, his prediction is likely also correct.