I am using both of them without any problem.
The main advantage of Flatpaks (and things like AppImage) is that you have a single "executable" with everything you need and sometime that is useful even if the software is Opensource but the building dependencies are a nightmare. Subsurface (a dive log software) is an example.
If the AUR package is a simple build (or a binary which is a converted package) then go for it. If you need to start building a lot of additional package from AUR to meet the dependencie then I would suggest, in order, to look for the Flatpak (or AppImage) package or to install an helper to build the packages
The two features are not mutually esclusive. I owned an S5 which was waterproof and had replaceable battery more than 10 years ago. It did not seems too hard to do