I've never heard of Onmyōji, but I think you did a good job of explaining through the narration and agents' dialogue how far from canon this fic got. I can see what the author was going for, basically a trans-dimensional snatching to take Ichimokuren out of the video game, but using the in-universe term "human dimension" makes it pretty confusing. It is nice to see zookeepers show up in a fic for once, although wow do they seem to have a lot of time to chat at work! I'm a little sad that Uminari's keeper identity got erased by the reality room, but oh well.
As a general note about your spin-off, I like that you use the actual fic's chapter titles as dividers. It reinforces the feeling that the agents are actually in a story, and that they're more at its mercy than they are within their own narrative.
There were a few sentences I noticed where you had dialogue end with a period when leading into a dialogue tag. A comma should be used there instead. these are the ones I caught:
"'Kaguya-sama, I think I am about to barf.' Momoka added weakly."
"'We will explain later.' the man said to him."
"'Many warm greetings to you.' said Kaguya as though . . ."
"'Everything is fine.' said Kaguya."
—doctorlit, about to go zookeeper within the hour