So, we are working on this, not just with Flatpack, but with a broad initiative we call "Modularity". (I know that's not the best name, but naming things is famously one of two hard problems in CS¹.) The big problem in operating systems in general is "too fast + too slow", and we are aiming to solve it. See https://docs.pagure.org/modularity/ for background on this initiative, or https://www.youtube.com/watch?v=xqZftb2Wgi4 if you like your information in video-presentation form.

1 . Along with cache invalidation and off-by-one errors, of course