I personally still prefer native, but flatpak is my goto for whenever something isn't working or when the official repos are outdated.
The other day I tried to use Malt for blender but it wouldn't work on the native version because it was using the wrong version of python. The flatpak version works perfectly with Malt, but for some reason I don't feel like troubleshooting, the OptiX denoiser doesn't work.
Still though, flatpak is a welcome option and is way better than snap.