I believe that scientists do not ‘empty out’ the donor mare egg. They extract the nucleus, I believe, and replace it with the stallion’s cell nucleus - which has his DNA. The donor mare oocyte already has all of the machinery in place to go through the process of going from one cell to an embryo and then a foal. If the nucleus was not “replaced”, the oocyte would be primed to start going through the motions of becoming an embryo and then a foal.
Yes, the foal would not have the stallion’s damline mitochondrial DNA, but there are so relatively few genes transcribed here that I would be very surprised if mitochondrial DNA contributed much to overall performance of the horse. Given the complexity of factors that contribute to the performance of a High Performance horse.
I agree that basically, breeding to Gemini Twist IS breeding to Gem Twist. Even if a person breeds to Gem Twist there is much that happens to gene expression patterns during every single cell division. The pattern of division and gene interaction/modification is a crap shoot and any uterine environment is also a factor. Breeding to a clone is breeding to his genes - which is what all breeders do. Of course there are other factors in the making of the horse and is why not even full siblings perform or look the same.
Laboratory animals such as mice are cloned quite frequently and can be indistinguishable, including their life span, from regular mice. Transgenic mice and “knock out”/“knock in” mice are created all the time. The technology is more advanced than some here might think.
It is true that there may be unseen factors when breeding to a cloned stallion. No one will know until it happens in large enough numbers. But there is really nothing predicted in the ACTUAL BIOLOGY that predicts that babies derived from clones will be significantly different from babies derived from AI or live cover. Lets not forget that lots of problems happen with regular pregnancies, too.