Even if it comes from the assembly line, it is the manufacturer's plan to want the moly to remain in the oil in the final delivered product.
You see, if it is harmful, they could have added a step to do an oil flush to drain out the moly. Cost them labor and oil maybe $3-5 per car. Yes, multiplied by X cars it would cost more yada yada...
But, at the very least, it is not harmful and probably beneficial.
Have you ever thought of the case, say the manufacturer wants moly in the oil for break-in, but they use moly in the assembly lube and they know a lot of moly will remain within the engine surface. So they order the break-in oil without the moly, knowing when the car is delivered, the oil will have plenty of moly in it?
Another angle is, if it is so random, the ppm of moly in break-in oil will be all over the map, from 500ppm to 3000ppm, right? I don't think it's the case, even though there aren't many break-in oil VOA or UOA.