“Genetics are tricky. There are so many things we do not know.” This.
When my twins were born, we learned that they are identical. That means they both came from a single egg that split. Shared a placenta. But while they look a great deal alike, they are by no means exact copies of each other. I could tell them apart even when they were infants, though others could not, including their dad. As they grew, they had periods where it was nearly impossible to tell them apart unless they were standing right next to each other.
Now that they are adults, I think most folks who know them don’t have any issues telling them apart. But as their pediatrician said to me when they were quite small, “Who knows what nature can do with the same DNA?”
So clones having different markings, is not surprising to me. But I also think it’s possible they could have different ways of going, temperaments, etc. I don’t think, based on what we know of equine genetics today, that cloning is a guarantee that you will get the same horse you started with. JMH(and unscientific)O.