EDIT to add: I also think packaging up an application plus the compatibility layer using flatpak[0] is a really nice idea; it lets you 1. make those apps available in a way that nearly appears native, 2. lets you get users/testers on your compat layer easily, while 3. scoping it to a single app at a time to make it easier to do things like "well we've got this one app working, but how do we tell people that without them expecting other things to work that aren't implemented yet?". Excellent symbiosis:)
[0] Strictly speaking there shouldn't be anything requiring flatpak here... I think there's no technical blocker preventing you making a debian package for the ATL and another for NewPipe and sticking them in a repo/PPA that people could add. But I do somewhat feel that flatpak lends itself to this usecase.