My specialty is the Ampeg Scroll Basses from '66-'68, and I can tell you that I've seen several Ampegs with original fingerboards that sure appear to be padauk. They aren't as bright and colorful as a fresh padauk board, but they are 45 years old.
It wouldn't surprise me at all if Fender used some on some instruments. Remember, back in those days, hardly anyone cared or thought about particular species of wood used. If they were able to buy a log of some interesting looking wood, they'd use it.