Q: During the Shirou VS. Rider scene in Saber’s route, why didn’t her daggers kill him? Was it because of the holy sheath embedded within his body? Or was it because his body had begun its swordification?
A: At that time, Shirou’s self-healing had already begun, but the nature of his regeneration was really quite indirect, “changing his muscles into blades in order to knit his wounds with swords.” That is actually what happened, regardless of what you saw during the scene in Saber’s route where Gilgamesh dealt him a mortal wound and Shirou appeared to have “masses of blades shaped like muscle fibers” in his body. So, Shirou’s innards are extremely durable. During the fight with Rider, she was able to injure Shirou with her stakes but it would have been more difficult and troublesome to fatally wound him, so she decided to kick him out the window instead.