At the time there was a lot of speculation as to why the vinyl tops were on the Penske cars. People suspected lots of different reasons. I think one of the stranger hypotheses I've heard was that the vinyl top covered up tiny holes which released air pressure from inside the car. I don't think I have heard anything about a lowered roof but bondo and paint can cover up welds as good as any vinyl top can. I believe Mark Donohue was the one who stated that the vinyl tops were to cover up wavy roofs because the bodies of the two team cars had spent a little too much time in the acid tank. Yes, a normal unibody structure would suffer a lot from too much acid dipping and the roof does strengthen the structure of the body. However, don't forget that these cars had complete roll cages which attached to various parts of the chassis such as the front subframe, the rocker panels, the rear frame at the suspension pickup points, the side panels just aft of the door openings and it was also welded to the inner roof structure in a number of different spots. This is what became the birdcage type of frame for the car which was much stiffer than any unibody car, especially one without a B pillar behind the door, could be on its own.
Eventually, during the 1969 season the protesting of the vinyl tops got to be so much that Penske did have to have them removed and my understand is that the wavy roofs were cut off the cars and new roofs were rewelded in place, sans vinyl. It is a good thing, since Penske's cars finally started winning races with the vinyl tops off the cars and they went on to win the Trans-Am championship that year, making it two in a row.
The author that mentioned the holes in the vinyl roof was being hypothetical, theorizing on a what if for what advantage a vinyl covering could provide. As it is if Mark stated in his book that they dipped the bodies than that is probably a key reason for putting vinyl on About 13 or so years later the theory of relieving aerodynamic air pressure was evident on World Superbike championship motorcycle fairings. Secondary benefits would be as Penske stated. The cars sure were noticed. Vinyl roofs would make the roofs look the same for little relative effort. And both men were being factual.
Last thing, vinyl is way lighter than metal, and probably equal in weight to the weight lost by dipping. The main idea though, is the solution to the waves was cheap, fast, and simple.