Oh my, so much going on here...first of all, I do understand that. Though I thought it blatantly obvious that, should Apple forego the Core Technology Fee for apps outside the App Store, literally every single large developer (and many, many small and mid-size ones) would leave the App Store so they wouldn't have to pay any fees; it would be a no-brainer. That would be the absolute worst-case scenario for both Apple and for iOS users.
Any developer choosing to list an app outside the App Store has already taken advantage of years of Apple's developer support and infrastructure—countless APIs, documentation, developer sessions, Xcode, etc. The $99 developer fee is self-evidently a de minimus fee that prevents spam and abuse—it has never been a fee for use of Apple's resources.
If it were such a fee, it would undoubtedly be much higher, thus boxing many small developers out of the program entirely. Unless it were based on the size of the developer, in which case we're pretty much right back to where we started.