the main drawbacks I see are related to the sandboxing of apps, e.g. that several firefox addons that I just, such as the KeePassXC connector don't work in flatpak packaged firefox, because they require native messaging support which is unavailable in flatpak. There is a three year old bug report on this at github, and an even older bug report in the Firefox bugzilla. Unfortunately, there seems to be no capacity to solve this or this is not a priority, although this problem affects quite a few users. I have similar issues with the Flatpak packages Nextcloud client: Do to the poor system integration, neither autostart works not integration with Nautilus or other file managers, unless you do some manual tinkering (which isn't particularly difficult, but with native packages it will just work™ out of the box.) These issues have been known for many years, yet there seems to be no activity to solve them.