An AUR package has been done for Arch by (supposedly) someone who knows what they are doing and needs it on their Arch Machine
A Flatpak is something done by someone, to (supposedly) work everywhere, untested on Arch, that may or may not work. And crash (Ardour on Asahi). Or waste hours or you life to render files incorrectly (kdenlive on arch and asahi).
Native versions work perfectly.
I thought I was clever in using arch/aur for everything, but pull KDE or QT apps from Flatpak to keep my gnome install a bit more tidy… For this, you’d have to have those Flataks to work, and sometimes they don’t.