I can only speak for how it was done at American Motors ( remember them!!!!!!!!!) when they were in buisness, I would think (IMO), it was the same for all car manufacturers. The firewall and any and all holes or openings were pierced at time of stamping. Any of these holes or openings not required, were then covered at the operation stage in the building of the car. If for example there was a opening required for wire looms that were not being used, they were plugged at that particular work station. The non-required holes were covered before the paint process at American Motors. This information was read off the broadcast sheet.
Dave