Ahem… minor correction if I may: “Because most of those apps…” 
Partially. Believe it or not, there are fully FLOSS apps in my repo where the authors explicitly stated they want them there, and not here.
True – and get removed once they reached “F-Droid proper”. Though many remain in my repo.
That said: Indeed quite a lot of apps don’t meet the stronger criteria at F-Droid.org – which is why they’ll never show up there. So I fully understand my repo isn’t included by default (we’ve discussed that before). Though: there could be a separate section in the “repositories” screen, stating something like “danger section” (with a short explanation), where such repos like mine could be pre-configured but not enabled by default. Not only mine – I also think of repos like Collabora, Bromite, Libretto…
Why not? Even Debian doesn’t hide its nonfree the way we hide 3rd-party repos 