Shortcuts are a way to move between rooms that are farther apart, like a trapdoor and a tunnel or something. It can be added later if I choose to, though it might cause a mess with the pathfinding.
Making rooms of various sizes requires quite a bit of code, and what I did right now barely requires any. What I have now is a 2d array that stores the bitmask, though it could just as easily be just 0 no room, 1 room. It is a nice feature to have, and may really upgrade the look of the world, but it is not necessary for gameplay, so it's pushed down the the bottom of the feature list.
Considering how often pathfinding woes are brought up as an issue, even in AAA games, I can only imagine.