I prefer native builds when possible, since they tend to be more streamlined and tailored for my distro (e.g. window borders, colors, and buttons all match).

But Flatpak is a good fallback. It’s a lot to ask of maintainers to keep up more than a few builds, at least on small / low-budget projects. The occasional permission issues are a minor price for a huge convenience.

IMO apt, pacman, and Flathub are all about equally straightforward to use once you acclimate a little.