Welcome to the quagmire of BATFE regulations.You'll never get a definitive answer from BATFE. And, even if you did get one over the phone, it'd be worth the paper on which it was written. Just like the rule on how many sales of guns does it take to constitute being in business, it is left open to the interpretation of the BATFE Industry Operations Inspector or Agent. They'll know it when they see it, and the judge will take their point-of-view long before he'll take yours, most likely.
I am not a lawyer, so don't take my opinion as sound legal advice. However, were I in their shoes, I'd tread ever-so-lightly in regards to what and how many they build. One thing I would definitely do is put a unique serial number on each one of them. In fact, I would label each of them with the word "Prototype," followed by a sequential number. And, if more than one was built, I'd ensure that each one had some unique quality or characteristic about it, so BATFE couldn't argue that they were mass producing the same type of gun. I'm not talking about different color MagPul stocks and grips, either. I'm talking different calibers, different barrel lengths/twist rates, etc. And, for each unique specimen, I'd have a written synopsis of each unique characteristic and what is being tested with it. I'd go into why the characteristic was chosen, what is hoped to accomplish, and more-as detailed as you could possibly be. What I would not do is transfer the prototypes to anyone not employed by the company in a research and development position. In fact, anyone who is being used to test the guns would be listed in the R&D document, along with what they are responsible for testing (long-term barrel life, concealability, ease of use, etc.).
Once the R&D is complete, so long as the company doesn't have an FFL, there is no prohibition against transferring the guns to someone who is not prohibited from possessing a firearm. This is one good reason, though, for putting a unique serial number on each one. An unserialed firearm manufactured after 1968 is not supposed to be built to enter the commercial market. Even if they aren't taking money for the gun, BATFE could very easily argue that services rendered in testing were payment for the firearm. (Internal revenue code would back them on that, too.) A non-licensee can make a firearm and subsequently transfer it, if they wish. Take, for instance, the act of making a Title II firearm on a Form 1. There's no law prohibiting the transfer of it later, so long as the tax is paid.