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)