They absolutely are involved. Apple views distribution of unknown compiled binaries as a serious security vulnerability, both because they can access private APIs that the App Store would otherwise block, and because Apple has no way to shut down an app distributed this way that turns out to be malware.

If the app is open source, you're free to compile it with Xcode and install it on your device. That's fine, because the open source nature means you can see everything the app is doing and verify that it isn't malware (and if not you personally, then someone can do it).

But for closed source distribution, barring enterprise distribution, it has to go through the App Store. Allowing anything else opens up Apple's customer base to malware.