Flathub is not the entirety of Free World, just a little small slice of the pie. You can say Flathub is quite centralized. But our Free World have so much more. Every country will have a certain focus of what is freely available. It's an optional server and package format. You are free to install it or use another free package. Nothing crazy here.
Flatpak was designed to be decentralised, Flathub is just the main repository offering flatpaks and yes, probably 99% of all Flatpak applications are downloaded via the main repo but it is technically possible to just launch your own if you are unhappy with the main repo. The Flatpak team literally has this info page for hosting a repository
I for example, am taking AAGL from their own flatpak repo because they are not offering their launcher via the main one (even tho they also tell you to link the main repo - I guess for dependency reasons - but theoretically you could open your own repo and throw all dependency related packages in there or am I getting something wrong here)
I agree with everything you said, however there are a few details.
it is technically possible to just launch your own [repo]
The ability to create repositories ≠ from mirror existing ones.
Unlike apt repositories Flatpak ones aren't simply a directory tree with a bunch of files that can get mirrored using rysnc or other efficient means, it's a clusterfuck of HTTP-only requests that need to be backed by specific metadata and there aren't tools to manage those.
flatpak create-usb may be promising but the name says its all - the priority wasn't to create a way to mirror repositories but a quick and dirty hack for some situation.
theoretically you could open your own repo and throw all dependency related packages in there or am I getting something wrong here
Theoretically yes, in practice things are bit more nuanced. That tools only considers your current architecture, it's a pain to get dependencies in an automated way and most of the time you'll end up with broken archives. You'll also need to hack things a lot.