Between this and Testflight, I get the impression that Apple wants to rule its app ecosystem in the feudal sense. Whatever "indy" contingent there is, it is just meant to effectively be the bush leagues for the major league, which is Apple itself.

Hopefully, Apple will realize that it's sometimes better to co-opt than to control, especially when what you'd be trying to control is an ecosystem experiencing dramatic growth. It's this kind of realization that resulted in the iOS App Store in the first place.

That said, Apple is in a good position to continue its feudal rule, for now, as (IIRC) Apple's income is far larger than that produced by the App Stores in aggregate. This would be analogous to the late Middle Ages when the rise of the merchants began, but their wealth and power were still dwarfed by the feudal power structure and the church. The merchants were useful to the existing power structure, but still had to kowtow to it.

So the way to defeat Apple, if that's what you want to do, is to foster the growth of a better ecosystem than the iOS App Store. (Or, it could be worse, but still bigger, unfortunately.)