1. usually ~/.config/PROGRAM_NAME/

You probably want to look into $XDG_CONFIG_HOME 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/

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