Apple App Store submission for an app that requires its users to be registered
An app I made for my company also uses an external program to register users.
To avoid possible problems with apple I did the following:


Created a demo database that apple can use
In the "notes for reviewing" I explained the authorisation process
I said that if they want full access they should email us the authorisation code generated by the app and we will grant them access.


In the end the app was approved and I never got a request from apple for db access.
As long as you explain in detail how the app works, apple won't give you any trouble I expect