This is why I take it to be a more abstract, less linear story than Spiral. I mean, for the love of god, he had to fly in a whole other person who wasn't him, who was outside of his head, who couldn't possibly grasp the intention behind each track as thoroughly as Trent himself, and let that guy put it in order. It's bound to be abstract! A collage, not a chapter book.
Maybe not the best word? But if you consider "The Great Below" and "Underneath It All" as speaking about/to an ex-lover, he or she has clearly left. The "you and me, make it through" on "Somewhat Damaged" becomes a pretty obvious reference to the "you and me" who are in things together in, uh, "We're in This Together." And that song is exceedingly desperate. Like he knows things aren't going to last. Someone on ETS once suggested an unplugged version of the track. I argued and said that would change the entire mood. I was rebutted and suddenly saw the song in a different light. I'd never considered how hopeless that vocal sounds. Like when your relationship is clearly dying, and all of a sudden you start saying "I love you" every eight minutes.
When the reverse was suggested above, this was the first thing I thought of. I've never tried that. It doesn't work out well in my head. But who knows. I'm wrong a lot; maybe this is one of those times.