Technical stuff aside, a major reason why Flatpak does not get the hate Snap does is because users don't resent it.

There are 2 things people hate: the way things are, and change.

Ubuntu put Snaps on users desktops without asking if they wanted them. They just did it, then closed off ways to opt-out/avoid them (Cf. Firefox).

Forced change fosters resentment.

No distro made Flatpaks default/required/opt-out. Users had time to come to the tech and adopt it on their own terms/needs.

Just IMO.