I don't understand what is it that you're asking, because you seem to reply to your own questions yourself… do you want to know what we think?
>What are the places that madotsuki travels to in the nexus?
That's a rather difficult question to answer because there is not a single answer. They could be anything, really, and everything depends on other factors. They could be memories, tied to real life experiences, just as they could be fictional places created by her mind while asleep. There isn't a single hint anywhere.
>Also the creatures that inhabit those areas are almost always an animal or some abstract being besides poniko
There are a few more that are anthropomorphic. Namely, the mall people, the guy fishing, and the people at the barracks, if my memory doesn't fail. To me, their design is simple only because they aren't tied to somebody Madotsuki knew, unless like Poniko who seems to be someone important enough to be differentiable from the rest. Also the toriningen. They're quite enigmatic, since they are well-defined beings with a rather specific purpose and states, unlike the others NPCs.