flatpak should really push to make it work better for non GUI apps.

right now its a total mess both for users and developers. IIRC apps cant register a command line alias that gets added to your PATH and theres no way to request permissions for a file by name (you have to open a file select dialog scoped to a directory). i dont know if you can even tell the runtime to open your app in a terminal without hacks.

its all pushing devs to opt out of sandboxing as much as possible which defeats the whole purpose of containers.

Flathub (not sure if these are the same people behind Flatpak) makes it clear they don't welcome these types of submissions:

https://docs.flathub.org/docs/for-app-authors/requirements