You may be right. And it’s even possible that the flatpak developers believed you were right.

And it mah still not have been the right decision because when it comes to products like Flatpak there are a lot of considerations beyond just what the best technically correct choice is.

For example, based only on your comment, basically every other OS does it the same way Flatpak does it. So if the Flatpak developers had done it the technically correct way like you suggested, it may have been enough of a burden for app developers, especially multiplatform app decelopers, that they wouldn’t have used Flatpak in the first place.

By this argument, Flatpak should not exist at all. If it does anything differently that is bad and if it doesn't do anything differently, why exist?