At the end of the day, they’re just different ways of reaching the same goal: universal packages for Linux. I personally use them interchangeably depending on the application and use case.
There are some packages that definitely work better and are intended to be used and installed via your native package manager (if they rely on system libraries and whatnot). But using either a Flatpak or AppImage results in the same experience - in my experience. It’s a personal preference.
In my opinion, Linux Mint has filled this gap. If anyone asks its a good recommendation to ensure they don’t have to jump through hoops to get a stable system out of the gate. Essentially the stability of debian and usability of Ubuntu without snap