You can compile and sideload any software yourself using XCode and an AppleID. I run Gamma Thingy (a f.lux alternative) on my non-jailbroken iPhone. You can compile and run emulators, use any private API, whatever. Those apps will just never be in the App Store.
It is a good point. I recently got a company provided phone and I strongly considered getting an iPhone, especially since it's the dominant platform at my company and most internal apps are developed for it exclusively. However, I started tallying up what functionalities I would have to give up and decided against it, a flux like program being one of them.
You can compile and sideload any software yourself using XCode and an AppleID. I run Gamma Thingy (a f.lux alternative) on my non-jailbroken iPhone. You can compile and run emulators, use any private API, whatever. Those apps will just never be in the App Store.