There is quite a bit of debate on this very issue with some GTO's. There are only a few documented 68/69 GTO's with the area around the rear tail lights blacked out. Some know this was the way it was delivered, and have kept it this way when restoring them... But there are many out there that don't believe this to be true...

Personally I think there were some dealers out there doing this, and possibly a few were given a slightly different treatment from the factory for show/display cars etc. Hard to say what is "correct" But it's your car, and it sounds like you have some compelling proof that it was delivered that way... given that, I'd redo it as it's shown!

Great question and I hope we hear more on this!
I also know of a couple delivered with a slide back ragtop sunroof that the dealer had installed for customers... interesting!

Brett - 67 Drop Top 455!