I have 1.5 thumbs and only about a quarter of my left thumb actually prints. The cops always warn me that my prints may not be accepted whenever I fill out a licensing application or an NFA form. I'll let you know when my next set of forms comes back, but I've never been rejected in either the print or scan versions of the FBI card before.
My bet is the NFA examiners look at the finger print form for all of a hot second before moving on to the other forms.