It likely won't ever get an official Wayland extension, for a number of reasons. Screen capturing is inherently insecure and so it shouldn't really be happening over the Wayland socket. It also doesn't need to happen over the Wayland socket or be related to the windowing protocol at all, attempting to do it that way is just re-accumulating technical debt left over from X11.
>I fear that this means if flatpak does not need a feature, even if it makes sense in another context, it probably won't ever be implemented.
I wouldn't think of it so much as just flatpak, but the API needs to be usable from within a sandbox, and it needs to be done in such a way that it can be reasonably presented to the user.
>For example something I require for my project are proper window names and their position
This is a really bad idea, don't do this. This is guaranteed to mess with the window manager and run into any number of syncing issues with window sizes being reported incorrectly. It's also a misuse of the screencasting API. I checked the issues you posted and I don't think you're going to get much farther trying to hack around the API. If you want to do this right now then you'll have to integrate with the specifics of the window manager or shell. There is no way around it, I really doubt you will get much interest in doing it another way.