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Hi Firstgen, I don't think it's common pratice to put all of these marks over the black paint, I think it's more of a reserch and documentation interest than anything, There are a few markings that will be over the paint though.. B T P stamps and the color callout T U R.
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I've seen many cars restored with these codes on top of the paint.
Most originals I've seen had the paint color (TUR in this case) under the firewall paint. Often visible since the letters (ie grease marker) seem to prevent the firewall paint from adhering correctly (and often allow minor surface rust).
Most common for being on top of the paint is the sequence / rotation # (used to track the car down the line) and TBP inspection stamps (NOR cars only).