It doesn't make any sense to adulterate any finish product used in production. Ford took things seriously and the engine color was used to identify engine assemblies. To adulterate or contaminate one color with a different color ruins its objective. What was known then as it is now, different batches of paint product may have shade variations from the manufacturer of the product. They didn't have computers matching colors back then. They just has emloyees following a mix recipe of different pigments to arrive at the color needed for the batch. If that recipe wasn't followed to a T then the batch will come out with a variation in shade or color. As long as it was close, it was good enough to use. If it wasn't,then it was either returned to the manufacturer or used for some other purpose.
If spray equipment was used then it was likely used till the source container was empty and then a fresh batch container was applied. Whether they had left overs or not is not known to the public so it would be information held by the employees that were responsible for maintaining the paint supplies and spray equipment. Engines were painted as separate parts as far as all the information that I have seen. This is evident by the lack of paint on fasteners that held the engines together.
Paint facilities were known to get a build up of what they referred to as Fordite on the floor or work station areas that had to be chiseled off every now and then to clean the area. Engine parts were likely processed in their own paint line area since the color was always the same. Sheet metal parts that were painted black likely went on a different line to keep from cross contamination of the painted products as well as spray equipment for those products. There have been a lot of rumors spread around about Ford processes but I would have to hear it from someone that worked in those facilities to believe the rumors.