You'll most likely have problems. In my experience the space for the weatherstrip is waaay tighter at the rear than at the front -- it's not a consistent gap like with a stock steel decklid. If you use the stock weatherstrip you won't be able to get the decklid to close far enough to fit right with the quarters and quarter extensions, and if you use something thinner it won't be thick enough to seal along the front edge.
This was my experience with a Shelby-style decklid, and there are many brands of 'glass out there. YMMV. Look at the 9,000 mile original '67 GT500 in the August Mustang Monthly and you'll see the decklid sitting 1/4" higher than the quarter extensions. This is how they were from the factory and I've seen it countless times. The best thing to do is to put the decklid on the car WITH WEATHERSTRIP before paint & body and rework the decklid & quarter extensions to fit right.