It just seems like it's a lot of papering over a fairly substantial problem. While the example I gave was Handbrake, which does seem like it should be a unique example, every other piece of software that I check Flatpak versions of also had ludicrously wasteful storage issues.
I'm aware of dependency hell, but it seems to me that most software doesn't have that as a problem, not if the libraries are sensibly maintained? After all, the fact that upgrading a library can improve all the software that uses it seems like it's usually a positive thing. And the ballooning storage requirements of Flatpak make it a tool that should be used occasionally, rather as a primary way to release software. Using a filesystem that can detect duplicates would help, but itself also seems like a special-case kind of solution, and not a great solution to turn to just to avoid what seems to me to be a significant issue.