Yeah, they sometimes have their downsides for sure. The darktable Flatpak does not work with GPU acceleration for AMD cards, which is extremely unfortunate. I have to use the official AppImage with the aurora-dx image, which includes doodads for graphics. Rebasing from the aurora image to aurora-dx was a cli command and reboot away.
I really wish Flatpak succeeds as the dominating software distribution format though (it probably already has), so I’m going to keep dog fooding whenever I can.
The man hours spent to keep every distribution specific package and repository alive seems like one of the worst waste of resources in the world of Linux. And I obviously don’t say that to diminish the amazing work that package maintainers have done over the years… I just think the time could be spent more wisely now that well established alternatives such as AppImages and Flatpaks exist.