You can store all the room layouts in an array yes but you'll come across a problem that the exits don't sync up if you're creating it in advance. Not sure how people would solve that problem. I made something similar when on exiting a room it created a random room during runtime.
Hmm yeah good point, I've just gone for all the exits & entrances are the same size so line up naturally, but I guess you could take the position of the empty tiles in the first column of the next tilemap & erase the end tiles on the previous to match up? This is for the way I am using the tilemaps, all in a row left to right, no idea for randomly placed ones. Perhaps lining them up based on imagepoints or something.