I lived in PR for years and understand your passport confusion. The answer is that technically on the PR to FL trip you are correct - she doesn't need one. But stopping the NAS will automatically negate that. She now needs one. Entering the US at any FL gateway is difficult without a passport, now you're either going to tell them you went to NAS and there's trouble, or you're going to lie and there may be bigger trouble. Even if it's PR to FL any cranky customs
guy could make your life miserable for a few hours while he figures it out.
Personally, I wouldn't want to start out my new adventures with my new boat like that. It's not the answer I would want to hear either, but unfortunately it's probably so. She should have the passport.
Good luck with your new boat!
On edit - does she have an enhanced drivers license