"Why do you ask that now?
Matou Sakura's body was tampered with many years ago. The changes were so extensive that even her hair and eye colors no longer reflect her heritage. This did not start recently."
"Well, it seems it was never intended to kill her as it's doing now.
It seems Matou Zouken did not intend to use Matou Sakura in this war. She is not adjusted to fighting. I would assume she was treated that way because unexpected conditions were met."
Considering Zolken wanted her as a future vessel and to produce a suitable heir for the Matou to fight in the next war it is incredibly likely that the alterations to her body where genetic and not simply cosmetic, in order to insure the whole reason she was adopted and produce a heir of great potential.
It's pretty clear he did alter her somehow, but I don't think he necessarily needed her to be a Matou genetically to use her for breeding, and I don't see how he
could alter her genetics in that manner. You also can't "gradually" change someone's genes like that, the fact that it's a gradual change implies some weird Nasu biology.
Your logic is that he used his worms to secrete a virus (which is something that was not even known about when he was making the things) in order to alter her genes (which were
also not known about) in a manner that we cannot even do
now that did a perfect job of turning her into a Matou (which isn't even a defined concept) without any significant side-effects by sheer chance.
I find it more likely that he did something magical to her that would affect her body, but not her genetic make-up.
Also, still don't get why her son can use her Element, Element's are generally unique to the person, and while families can be more likely to have specific one like the Aozaki's know for having wind element special elements, like being an average one or unique traits such as multiple elements are not passed on.
Well, he can't use it much. His main element is ether.
And if you say it is a crest then do know that implies Sakura converted her own circuits into a crest and passed them on, a very dangerous process even for blood related children.
Erm, what? It's the standard way of making a crest.
You mentioned he has some capability with projection I understand his dad had the tailor made circuits for that so I can let that slide (but on the other hand I believe Nasuverse magical capabilities are kind of randomized as I don't exactly see Rin and Sakura being to similar to Tokiomi beyond the direct crest inherited stuff) so he may have some better affinity that most magi I do have to wonder one thing.
Shirou's projection is only useful because he has the data perfectly stored in his soul so he can make detailed copies. Other people even if they are good at the reproduction process of projection don't exactly have the blueprints detailed enough to make anything of quality. Everything projected would honestly be up to the quality of what Shirou makes in his shed. Interesting as a magical concept with how long they last but all functionally useless in their original task beyond superficial appearance. So Mike what's the point of the projection skill?
Projection is actually a common skill for mages so the basic kind can go without saying I believe but the specialness of Shirou's type is exclusive to his soul and circuits.
His projection is only the standard magical form, which is most likely useless. What he is best at is creating ether clumps and manipulating those.