Mh. Much as I like the "wtf"-feeling of it, it also feels a bit random. "Yeah, let's just go with that, whatever..."
It allows for more interpretations, just like the wet dreams/masturbation stuff. Doesn't mean that was the author's message, who probably just wanting to do something weird, but it still is a fun activity.
I had time to think more about my own (silly) interpretation. Perhaps it has to do with the feeling of powerlessness when you want to help someone close, but you realise that you can't or that you are not needed.
We see the roommate struggling with nightmares before she splits, similarly to somebody struggling with their problems right before they decide to face them. Then the munching part is when they decide to attack them head-on, we could see the eating part as both fixing and accepting your problems. In the end, the roommate seems quite happy after she ate her other "problem" self : she made her problems go away since her other self doesn't exist in the proper sense, but in a way, her problems are still present in herself as she accepted them (literally) in her.
In summary, a problem arise in the roommate life (a nightmare), she takes a step back (split) to face her problem head on, she fix them (ate them) and accept them (digesting) - I think this a weak point of my interpretation, since I think you should accept your problems before fixing them, but why not. And after all that, she feels relieved or somewhat satisfied and goes back on living (sleeping).
Meanwhile, the MC is observing her roommate, somewhat fascinated by how she is resolving her problems alone, perhaps kind of frustrated because she can't really do something significant to appease her. She tried once to help her (nibbling her) when she was having problems (nightmares) but realised that it was useless, that "[She isn't] good enough." only leaving her roommate still struggling with her problem, who does seem to be still struggling in p10, when the MC failed to eat her.
In the end, the only thing the MC could do is watch helplessly as her roommate is dealing with her problems, no interfering, comforting her and being there for her when she has dealt with her problems - by caressing the belly which contains the digested other self (the problems).
The message could be something along those lines : the problems or the anxiety your friend/lover is experiencing can only be effectively dealt with by the concerned party, you can't deal with them (eat them) for the other. All you can do is be there to support them and help them "recover" somehow - this is illustrated by caressing the belly while the roommate is digesting, apparently it helps with the digestion to massage the belly in a clockwise rotation (by martial art energetic philosophy and perhaps supported by some scientific articles with more grounded results).
Of course, it's missing some important stuff like sometime you can be the one giving the nudge for the affected party to finally deal with their problem, and perhaps other stuff I haven't considered, but I'm quite happy with that!
Oh. Nice. My answer has a vague resemblance to this very nice take on it. And I'm usually terrible at these! Well. Still am really.