I think it’s supposed to be some story reason since at that point the hachina you’re controlling is her more benevolent side that forgot her past and simply wants to help humans, is fighting a version of her old god self’s ego that wants nothing but to destroy humans. By the time you get to that point. I noticed the god hachina sort of has aspects of youkai and bug in her design which were both technically enemies of the humans, so I guess it’s supposed to be something like the medicine you’re crafting is a manifestation of hachina’s desire to help humans/just a counter in general to bugs and youkai which is counteracting the god hachina’s desire to destroy humans/the bug and youkai parts
Spoilered it just in case some people still care about being spoiled for the final boss