Yes, the silver prototype had the scoops molded in, very similar to the way the reproduction fiberglass hood was (is), but the silver prototype had a slightly different shape to the scoops, more squared off. Pontiac molded that hood for the prototype, but decided to go with a steel version when it proved to be cheaper to stamp, they could maintain better quality control, and get a better fit and finish. The scoops on the 69 Trans Am steel hood were removeable.
In 1970, Pontiac ended up using a fiberglass hood on the Formula because those two long, tunnel style scoops could not easily be stamped in steel.
As a sidenote, the 69 Ram Air setup I was referring to above was cumbersome, contained many pieces, and was a one year only item. It used a small 9" diameter x 2" high filter
retained in the hood, and a screen mesh strainer over the carb for catching large debris, similar to an L88 Corvette. When Royal Pontiac prepped a 69 Firebird 400 for a magazine test, they discarded the whole 69 setup, and used a 68 Firebird Ram Air setup, which used the standard 14 x 3 inch filter mounted on a Ram Air tub base. Easy to remove, provided much more air, and arguably looked better.