The factory "Process Standard" paperwork I've seen & read, states the filler used under vinyl was a heat cured material. (Called Plasti-sol IIRC).
Similar to bondo, but as mentioned, more like the hardness of the factory seam sealer.
It failed miserably when moisture would get behind it through the open spot welded roof seam and cause rusting & filler puckering.
I've personally seen one or two cars with lead used under an original vinyl top, but I'm of the opinion that most were done with the plastic material.

The seam needs to be welded solid and pinhole free in order for plastic fillers to last.
I'm a firm believer in welding the seam solid and using lead filler on painted top cars.

More info on the lead vs. plastic debate here...
Leadwork 101

Rick