obviously good for the bit, but the serious reason why this exists is likely because it's a modern gtk app - it's meant for gnome users / made by a gnome users - gnome is all in on freedesktop/flathub - these users can all expect to have flatpak availability as a common method of distribution - therefore, release it as a flatpak, so these users who already have flatpak can more easily manage their appimage-only programs
Is this like a special branch? I know hajkey is the name of the modified calckey that is run by blahaj.zone, but unless I'm mistaken that's just what blahaj.zone is with no prefix
You probably want to look into $XDGCONFIGHOME and the freedesktop spec documentation if you are interested in more of where these standards come from:
https://specifications.freedesktop.org/basedir-spec/latest/ar01s02.html
(and more generally)
https://www.freedesktop.org/wiki/Specifications/