About yuzu is pretty much obvious. But characters such as Akatsuki usually follows a pattern. He probably does have a connection with paca and all of them, but I wouldn't doubt that the boy himself isn't fully aware of it or simply doesnt know. Or has forgotten, which is a possibility since it was implicated that he did meet yuzu in person more than once. With pictures of them in lab coats and all, but until now he hasn't given any hints of actually remembering. In other words, I wouldn't doubt that, in the end, he is just that good boy. Or he could have a twisted personality like you said.
Tho I think that with all the cliches we have had until now, the first option would be the answer. I also read one that the goody boye let everything out and turned out to be not-so-good. But those usually have a better background and a much better plot, so...
Okay I don't trust goodie good characters like Akatsuki at all... at this point I believe that he is friends with Paca or even family and that he is actually one of those weird animal hosts that own a district.... I wouldn't be surprised at all. Pretty much looking forward to when he does get angry for once because he'll snap so bad that the others will be terrified. Reminds me of another story i read with the Mc being Twins and having twisted personalities.
Also the long haired girl Yuzu... stalker and pretty sure she knows what's going on....