I just started a new game and I picked one of three bunks offered to me. I'll admit that I'm not very far into the game so far but I couldn't help but wonder if my choice is going to come back to me down the road. Does it matter who you bunk with?
It makes no difference, gameplay or story-wise.
It's simply the way the game does profiles. That is, each bunk corresponds to a different profile with its own save files, so multiple people could play off of one copy.
If you're actually using multiple profiles, remember to use the green door (load game) instead of the blue one (continue) when starting the game. This allows you to select a profile to load from.