Howdy Uboachan I'm new etc. etc. let's get on with it. (I dearly hope this thought isn't old and dead.)
I was reading through some older theories, and someone pointed out that the staircase with Kyukyu-kun on it leads to a door exactly like Madotsuki's, with FACE behind it. This makes me think that Kyukyu and/or FACE are representing whatever it is outside Madotsuki's door that keeps her from going out there. Something horrible and scary.
My theory: Madotsuki is being stalked, or thinks she is. Kyukyu could be that weird guy who stares at her whenever she leaves her apartment, creeping her out enough to give her nightmares. All the rape-related imagery in her dreams comes from her fear of that guy doing something awful to her, and the creepy eyes everywhere come from her paranoia/fear of being watched. Madotsuki is so terrified by him that she refuses to leave her apartment, going insane from the paranoia.
(As an afterthought, this could tie in to Poniko/Uboa as well- Maybe the guy was a friend of hers, or at least someone she trusted, before he started being a creeper and freaking Madotsuki right the heck out.)
Enjoy this picture of Kyukyu not being creepy. Found elsewhere on Uboachan.