Does the older cockerel knows if the chick is a male or female better than I do? Or was he confused and he doesn’t know the difference yet? or maybe I’m the confused one
Maybe, not sure to all three questions. Some chicks start puberty pretty young and I'm not sure how chickens tell the difference between males and females. I think there is a fair chance he knew it was a cockerel.
When dealing with immature chickens especially mating behavior is not about sex. It is about dominance. The one on bottom is accepting the dominance of the one on top, either willingly or by force. I don't know if that was willingly or by force. It makes sense to me that the older cockerel was establishing dominance over a future rival.
I don't know what differences is sizes there are now or will be when they all become adults. I don't know how many other chickens you have or what sex or size they are. I don't know how much risk those younger ones are in. The more difference in size the more risk in mating, but as long as it's not violent the risk is probably pretty small. Especially if it is rare.
What are your plans for those cockerels? You can separate them now if you want. But if you plan on them sharing coop/run space when they get older, your chances of them working that out peacefully are better if they are raised together.