Topless '66 Barracuda

Pretty sure the staples were for the top. Later cars rely on the adhesive, windshield gasket, and windshield trim to hold the front edge. I would just trim it so it is cut off at the flange where the window seal seats and make sure the adhesive it good quality (3M) and applied properly. That being said- I have not done one on this body style so if you can find one that has I’d give them a listen.
I agree with you - and will be following your advice. I was just hoping there was someone out there who had dealt with this before to confirm my (our) suspicion. It's strange there is not even a hint of old vinyl top material anywhere under the staples. You'd thing there'd be a little bit somewhere. There's not even ROOM. The staples are flush into the roof/A-pillar. This is one of those times that having a rare/oddball option makes things a bit more complicated. :)