Does Apple have administrative control over Developer program enrollment?
Yes - Apple has very good administrative control and you deal with the sales organization (online web store) when you are purchasing any developer account. They aren’t going to know the in-and-out of why you were rejected a bunch of times but they are showing you clearly the way forward.


Pay the $99
Get your account going now
Upload your first two or three apps to TestFlight and get your testing going with hundreds of internal beta testers. 


Then engage the developer support team for free once they can see the sort of work you’re doing and when you have a specific need the basic account can’t meet. Now you’re a known partner they can work with - now you’re the guy keeping on banging on the sales door that was closed again and again. True enterprises are easy to verify and when Apple isn’t sure you are an enterprise, their job is to say no and reject the application so don’t get mad at the process or the people - just level up your goals and build your app now and work with developer support down the road - once they see your need, they will be your advocate so sales arrange an upgrade and/or pro-rated refund if you really need to get to enterprise features before the first year expires.

https://developer.apple.com/programs/enterprise/enroll/

Since the test flight restrictions are so lenient now, you won’t need enterprise to distribute apps to hundreds of employees with the $99 program.

The enterprise account is really for people that start with a normal developer account and need added functionality. If you haven’t had one to two years of experience in the developer paid programs and are not actually an enterprise - I would strongly discourage you from going for the enterprise program out of the gate. You simply don’t need it to get going in my experience.


How to appeal rejection by Apple for Developer Enterprise Account?
I tried to enroll my company to Apple Enterprise program, but get message &quot;Cannot enroll in Apple Developer program&quot;