I don't understand Jeff, what different car are you referring to?
Here is what I "know" based on what you have already provided
"The front seat in my 66 convertible had to be removed to install the brake light switch. The car dealer said he installed new pony seat covers since they came with the car when he acquired it. The seat stud nuts has plastic wrap over them and all four we're torqued the same."
So we suspect that someone has had those floor pan plugs off it you found plastic wrap at the nuts above where the rubber plugs are originally located
"Are June 66 cars built in San Jose known for missing body plugs? There are a couple of plugs missing in a undisturbed original undercarriage and there is no witness of a plug."
You report that a few were missing and were guessing that it was not a result of the earlier access to the seat anchor nuts but instead a worker at the plant leaving them off. You would not normally see any damage to the floor primer/paint as a result of the plastic plugs being inserted nor a shadow unless the floor was covered with road grime, oil, undercoating and the plugs recently removed. If the plugs had been out for a while the road grime could be fairly even over the surface and hide that fact that the plugs had been there originally depending on the time gap between one and the other events
Since I now understand its the same car I think its fairly easy to accept that the plugs were removed, some got broken or simply forgotten when they got done with the task