You can't build a pre-ban rifle out of a lower that was never on the books as a rifle prior to 9/13/1994. Its a post-ban in that case.
The way it can be proven if it ever came up is ATF would simply track back each transaction from one FFL book to the next till they get to the place it went after leaving the factory. If its on there as just a lower before 9/13/1994, then you'd be on the hook to prove that it was in a rifle configuration before that date. Good luck trying to prove that since someone else owned it at that point.
I'm surprised Armalite said that about the EA, I've called them before with a s/n and they were able to tell me the month and year of manufacture and I think configuration. If I chose one it would be the EA. I've had both and the Olympic was just a little off when putting a non-Olypic upper on it. Both Eagles I had were fine though.