I asked this exact thing somewhere else, and the best answers I got were:

• there is a somewhat legitimate motivation for fedora to package their own flatpaks in the context of their atomic desktops project.
• they started doing this before flathub was established, and it was a better idea at that time.

So, as per usual with Linux, there are some obscure and historical reasons this is a thing, but it is useless for the majority of users. Fedora should really not have it configured as the default source for flatpaks out of the box