It fulfills a different purpose than system packages. First, it can be run without privileges/system modification, so it works on immutable distributions. Second, it doesn’t share libraries between apps (with some exceptions) or the system, so you don’t have to package separately for each. It essentially takes some of the container philosophy/tech and brings it to desktop apps. This also gives it some ability to do some sandboxing that isn’t as easy with system installed apps.
This approach comes with some downsides. Particularly larger storage requirement for apps, sometimes less integration with the system, and lack of ability for apps to easily call/interact each other unless they’re packaged together.
It’s meant for complete GUI apps and not small tools/packages that are the standard in system package managers
Yeah. It has easier sandboxing. You can accomplish most of the same things with traditional packages with something like apparmour, but flatpak has motivated the development of portals which allows apps to request permissions on the fly more easily.