@thibaultmol
I think I was able to do that with Droidify (an alternative FDroid app store with an extra app source), I think it sometimes try to cross-update, though I'm not 100% sure.

Other than that, as with Obtainium, I had to manually search each app (though that was worth it, I now get most of my App updates directly from the dev).

@thibaultmol you can get this information via our F-Droid client.

Go to Settings -> Manage installed apps. There you find all apps that are available via your configured repositories.

To check if it was installed via another source, you have to click on each app (or the ones you're not sure about) and scroll down. When there are versions available, it comes from F-Droid. When there's a text about "no compatible signature" it's most likely from another place.