I mean, said suit of swords is pretty tanky, both externally and internally.
Before the Artoria Alter fight?
Here, The flow of magical energy from EMIYA's arm is so potent it causes Shirou's bones to break.
Here, EMIYA's arm will reinforce the broken parts (the same way it has been with Avalon, his body is made of blades). Here, EMIYA's Unlimited Blade Works is invading Shirou's body the more he uses the arm, its already far enough along he can hear creaking sounds.
Before the Dark Sakura fight?
Here, Shirou's spent most of the magical energy in himself and EMIYA's arm, he thinks he can only manage one more projection (he can manage 2, really, but that's besides the point as Excalibur killed his ass anyway).
Here, Unlimited Blade Works turns Shirou's body further into swords, he figures he could repel bullets now.
Here, Sakura's refusing Angra Mainyu, it now acts against her will and keeps her alive.
Here, the Shadow attacks Rin, Shirou shields Rin's body with his own and he tanks the blow to his back.
Here, the Shadow's next attack grazes Shirou's cheek, Sakura's yell prevents it from slicing through his neck.
Here, Sakura tries fighting back against the Shadow, the only thing this does is increase their numbers.
Here, Sakura can't suppress the Shadow, the next blow grazes Shirou's cheek.
Here, seems like the next strike lands on Shirou's shoulder.
Here, the Shadow's pressure gets stronger towards Shirou with each step he takes.
Here, the Shadow strikes Shirou's stomach next, it fails to pierce, Sakura's intentionally trying to push Shirou away.
Here, Shirou removes the Shroud of Martin for the last time.
Here, the Shadows lance towards Shirou's chest, shoulder, left leg, and stomach. The Shadow can't pierce his body made of swords.
Here, Shirou's body of swords tanks 2 more strikes from the Shadow.
Here, Shirou projects Rule Breaker, he uses all the remaining magical energy he has.
Mind you?
Here, Cu Chulainn employs the protection of all of his 18 Primal Runes to defend against Angra Mainyu/Sakura Matou's Shadow's tentacle attack, the defense doesn't even slow them down despite being able to defend against a great Noble Phantasm (I imagine that'd be A rank given his Gae Bolg is only "average")
All this before confronting Kirei.
To note, his internals are also fairly durable whenever his body reinforces itself with swords.
Here Shinji Medusa hits Shirou's shoulder. Shirou's body had already started to self heal, so the muscles that were being knit together by swords causes Medusa's dagger to break on impact (ergo, that's definitely full force in terms of striking power). Medusa muses she can't kill Shirou with her dagger.
Here, Shirou endures a roundhouse kick from Medusa out the window (yet free fall from the 3rd floor is supposed to kill him... I'll find an author that one day understands how stupid this sounds after considering the previous 2 attacks).
Here, Gilgamesh attacks with Merodach/Gram's version of the attack Caliburn used to kill Herakles, Shirou's Caliburn goes to clash with it, Caliburn breaks on impact.
Here, Shirou's body was split from left shoulder to waist by Merodach/Gram's version of Caliburn's attack.
Here, Shirou's body was reinforced by UBW swords stitching it together enough that he was praised by Gilgamesh for his durability (as he was able to keep his body from being blown apart by Merodach/Gram's version of Caliburn's attack like Gilgamesh was expecting to happen).
...
Kotomine's martial arts does indeed target the internals, but those internals are pretty damn tough to be fair. He also needs to be something of a physical peer to Cursed Arm at Rank B to deflect his dirks and have his Black Keys throw his ass into the tree to pin him there. He's not a Servant killer, but his stats are on a level that can contend with them even in the 5th War.
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