Gnome-Builder, the official Gnome IDE, builds flatpaks. I'm not sure how good it works, but idea is that one should imagine this brave new world of Linux sandboxed apps similarly how IDEs could work on smartphones. In the end the IDE must be either blessed with special powers or it must build packages for the sandboxing system. Gnome-Builder seems to take the latter direction.

I had run it via X11Forwarding (I had a contusion and used a puny laptop to connect to my desktop) and it was not a smooth ride, so it's not an entirely representative experience, but it shows that it's not all painless, yet.