First, thank you so much for picking up the series. Is my favorite yuri at the moment, and I was going crazy with the English translations being abandoned.
Now about the twist, I feel like while Nekotarou put some hints here and there, I think it could've been handled better. As others as pointed out, the eyes are so striking that it just doesn't make sense no one pointed it out. Plus, Natori suddenly having played only the game up to the beginning of chapter 2 is such a lazy retcon.