Um... wait a minute, is that truly correct? I played through a true mercy route (a lot of work) and didn't fight Hyakki at all. Yes I have Hyakki in the dream space but i can't appear to see her loss scene that is experienced in the genocide route. Also there is another gril in the game that has a loss scene i think part of the way through chapter 4 that doesn't appear in my loss scenes either and i have to dig through my saves if i want to go back and see that for chapter 4. Now I can tell you that Anegorami has that fight scene in his save directory against Hyakki, so that loss scene is technically available to the community(?) here.
I don't believe I have any access to read through the Hyakki loss scene or the other loss scene in my saves uploaded or in the true mercy route in general, I'm referring to in chapter 4 (sorry for being a vague ass and I know this other particular one I'm talking about is NOT exclusive to one route or another as well) but I want to try and help give good answers. Also I think in the regular pacifist ending, you don't fight Hyakki ether though i could be wrong about that.
This game is a cluster of confusion Clawfoot, if you are going through the game on your own for a true mercy route be prepared to back up saves in a haphazard manner like i did i my uploads.