I only saw the episode the one time, but I feel like they explained most, if not all, of those supposed plot holes. It's not that everything got a deep and profound answer, but I felt that everything was addressed enough for me to just be able to go with the story.
For instance, about knowing what clothing is and needing it - he comments about that when describing his first transformation, that he suddenly became aware of his nakedness and knew he needed clothes. Regarding the "seduction" of Scully, he says being a human male makes him want to lie about sex.
Whole thing made enough sense to me.
Its pretty much a modern day version of the old Golem of Prague story. Basically the Golem (or bandaid man in this case) is still out there and will protect the Jews/Homeless when more servants of Rudolf II/real estate developers come in to attack their community.An entertaining monster-of-the-week episode, but it ended kind of abruptly.