Because one process will be running on the hardware, because of the way it works it can’t really share that hardware between processes. I’m not sure if that’s entirely a hardware limitation, but it seems to be enough of one that software hasn’t overcome it.
Not specifically. It’s probably actually a configuration problem though, for any other program I’d delete or default the settings. Not sure how to do that for flatpak itself as I won’t use it.
Check which version of ffmpeg it’s using and whether it has hardware acceleration for that codec.
Also bear in mind that you can’t hardware decode and hardware encode at the same time on the same device. If that’s what you’re trying to do it’s probably falling back on software silently in Windows instead of telling you.