On the audio production side of things it's actually pretty good. The selection is pretty comprehensive and the jsons on github are simple and clear enough that you can build your own for any they missed. They're versioned with the runtime so there's the usual September problem of program A having updated while program B hasn't yet, but that's the nature of the beast.
A problem that's less well-solved is situations like Cantor, where a single application is a front-end for multiple executables. To get it to actually work you'd have to package Scilab, Sage, Maxima, Octave, R, and Julia in the flatpak itself, and these are non-trivial programs to package. There are workarounds with flatpak-spawn, but at that point why not just install the application natively? (I think the "right" answer is to set up a dbus service for like "system-octave" or whatever and have a separately flatpak'ed interpreter register it, but as aesthetically pleasing as this solution is it doesn't seem to have induced me or anybody else to actually do it...)
How it is done can be seen with OBS: flathub has several OBS plugins available (com.obsproject.Studio.Plugin.*).