But that, as far as I see it, is the point.
She'll develop feelings for him but logically know that it can't last since she'll be graduating and more than likely moving away from B&R. So you'll see her continue to be his FWB, all the while swallowing her feelings and keeping up the pretense that it's just casual, even when the MC starts talking to her about other girls he's seeing. Until eventually, probably near the end of the game when he's now several months in, maybe into the 2nd semester, she'll explode like a pressure cooker and tell him she loves him but that it's stupid since she'll be leaving and he's just started.
All this will lead to the cliche "last to the airport", Can't Hardly Wait style ending where, if he chooses her, he'll go after her even though she already left and tell her that he's in love with her and doesn't want to let her go. Basically, this is what the Zoey flashback was all about; to foreshadow him not letting that happen again.
It's the difference between 'possibility' and 'probablility'. Your "possibilities" deal in extraneous details, often entirely made up details, and connect dots that aren't there, so the probability of them being true is very low especially given that the known details presented by the game are very contrary to your "possibilities".
Many of the things that you see as "suspicious" and that feed your theories of interconnectivity and conspiracy, often have very common sense answers or are entirely irrelevant elements of the game. There's such a thing as looking too deeply at this game and I'm afraid that's what you do an awful lot.