In general, I agree, but I don't think that the number of people who could re-write or bypass the factory triggering programming is any larger than the number of people out there with the machining experience and equipment necessary to modify current conventional weapons to full-auto.
Of course, you could have talented people making and distributing replacement chips that almost anyone could install themselves, but you have the same situation now - lots of people with the means to manufacturer illegal conversion kits that are drop-in (or nearly so).
I think the BATFE could handle illegal conversions of electronically-triggered weapons using their existing policies - "Yes, it can be done, and it's not even particularly difficult. Just understand that if you're caught doing it or helping someone else do it, it's your ass."