floor repair panels
do have the indentations for the plug areas. At least those sold by Walloth. In the middle of that indentation is a raised area, 1"x1". It appears to me to be a fixing point for the stamping process that later gets removed.
Karmann, BMW, and Porsche dip the bodies in a phosphoric primer bath. Bmw recently released a documentary , shown on the discovery channel, on the Z4 which showed the process.
Porsche showed the process in a film entitled, "made by hand" sometime in the very early 60's and is on youtube in the first part of several.
Both show essentially the bodies and parts going through an assembly line through an enclosed area, in what I call a large trough . Most of the body is submerged and more recently there are sprayers on the roof areas.
That phospheric primer is light grey/ beige. I always assumed that coating was what can be seen in select areas on some original cars.
My vote is a conservative approach- put it back as original as practical with the advances in corosoion protection now available from lessons learned .