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.