Ok, let me explain how things work in the automotive industry.
The blueprint for the part is the "bible". The parts must meet all specifications and dimensions on the currently released blue print for that particular part. If the specification is not called out on the blue print, the supplier is not required to meet that specification.
If he makes a part(s) that don't meet the blue print specifications and is something that causes an issue at either the component or vehicle assembly plant, it is now considered "out of print" or "bad". The part is then given to the plant engineer that is responsible for that particular part/system. He then takes it to the layout room and has the part measured to prove that it does not meet the part print specifications. The engineer then takes the out of print parts along with the blue print specification and the results from the layout room proving that the part does not meet the print specification and hands it off to the Supplier Quality representative in the assembly plant.
The Supplier Quality rep now contacts the company who makes the part and requests that all parts starting with the next shipment must be "certified" to make sure that they meet that spec. Usually they are required to put some sort of mark on the part to signify that it is "clean stock" and ok to use. They use a paint pen and put a slash/line/or some geometric figure to mark that the parts have been sorted and found to be defect free.
The supplier is also required to send a representative to the plant where the "defective stock" is to sort any stock that is within the factory walls. He then gets with the plant's production control department (who is responsible for all incoming stock) and has them tell him where all of that particular part is located in the plant (there may be more than one location). They then tag and contain all "uncertified" stock and either send it back to the supplier's assembly plant for "certification" or he is allowed to bring in a crew to sort and mark the parts in the assembly plant (especially if he can't keep the pipeline supplied with new certified stock). When each part has been sorted and seperated the good from the bad parts, then the bad ones get sent back to the supplier or if he sorted at his factory, keep the bad ones and send back the good ones. But they must be able to PROVE that they have sorted the parts. That is why they are required to put some mark on them to identify them as good stock and it must be easily visible. Any bad parts are marked with a red paint pen (red is the universal color for "scrap/no good" parts - also oranges and pinks are not allowed as they can be mistaken for red). All assembly line workers are trained not use the part with red paint marks on them.
Meanwhile the supplier is required to fill out all kinds of "who dunnit" forms. Five why's, fishbone diagrams, and root cause how the defect wasn't caught in his manufacturing plant and then he has to add a check in his process to not allow this to happen again. The supplier is then required to mark all stock for at least 30 days until he implements the new process to prevent the defect from occurring again. He must maintain his clean point for at least 30 days before he can stop inspecting and marking all incoming parts. If another part is caught with another defect, then the supplier is required to do the process all over again.
He will then be required to come up with a second corrective action on how this got out of his factory and place a second mark on the parts to show that they have been reinspected again. Quarantine all stock at the assembly plant again.
If the clean point is violated a third time, then all hell breaks loose. They go through the quarantine and certified stock process all over again. Meanwhile the plant manager and quality manager from the supplier's factory have to come have a meeting with the manufacturing plant managers, the buyer for the part and the buyer's manager etc to explain why they can't make a good part - very humiliating for the supplier's management and usually gets them back in line. If not, they will not get any more future business.
Another example may be the engine plant. Let's say that a few engines were found at the assembly plant (for the whole car) that had one loose exhaust manifold bolt. It was the same exact bolt in all cases.
Now the engine plant has to certify all engines coming into the assembly plant. They would place a guy at the end of the line who checks to make sure that that particular bolt is tight and then puts a paint mark on that bolt.
The engine plant also will send a guy to the assembly plant to round up all the engines and verify that the bolt is tight and put a paint mark on it.
Now on the engine assembly line, let's say that they use a person to tighten that particular exhaust manifold bolt and he uses an air powered pneumatic motor. The corrective action may be to use an electric motor to tighten the bolt and then tie it to a line stop, so the engine will not be sent out of that station until the electric motor successfully torques that bolt. Once the engine plant implements the new electric motor, and maintains marking the engines for 30 days without letting another "defective one" get out, then they can stop marking that exhaust manifold bolt.
It is these marks on the parts that the "survivor" cars document. They are a shap shot of what was going on in the assembly plants at that time. There may be more than one part with a paint mark on it for one particular vehicle. There may be more than one supplier screwing up the parts at one time. Cars built at different times will have different marks on different parts.
Another reason for marks on a part are for what they call a "running change". As opposed to changing at launch for the start of the new model year. If the change is not too difficult to implement, then they will write it as a running change. This can change at any time in production as soon as the change has been verified and approved. when the supplier is ready to make the change, he will then ship the new level part (the blue print is changed one level to reflect the change).
But a simple change may cause a problem in the assembly process. So the engineer at the assembly plant will coordinate a "test build" were the supplier makes some parts with the new change (could be 50, 100, 1000 etc). Then all of the parts are marked with a paint pen so they can be identified. The engineer and the supplier will then take the new revised parts to the assembly line and have them try them. They will let them run down the line and make sure that they don't end up in a repair area for some assembly problem (maybe interfere with another part, or potentially cut or pinch a wiring harness). If that happens, they stop using the new parts and "go back to the drawing board." If the parts run fine with no problems, they run out all of the test stock (all parts are good enough for a customer's car), and then the plant engineer signs off on the change and then the supplier can then go ahead and make the permanent change to his parts and necessary tooling to make the parts.
So the strange paint marks you may see on a new vehicle are a snapshot in time of what was going on in the assembly plants when the car was originally built. Altering these parts diminishes the historical value of the car as being a survivor and a reference for time period correct restorations. The perfect survivor car is the Hemi Cuda or Challenger that someone bought and then took home and stored in the garage and barely/never drove.