I've noticed that decouple is NOT just when the connection is made in the VAB. I built a station where I had 4 ports in a square facing the same direction; I had another assembly with another 4 ports in a square of the same size. I maneuvered the assembly to the station and "docked" it. It seems that every time I do, one of the port pairs has the "undock" option while the other 3 have a "uncouple" option. Thinking about how each structure/vehicle is a tree in the data file, it seems to me that the first port that connects acts as the root for the branch you're snapping on to the tree. The other ports that dock secondarily forms a link between two branches in the tree, and get the uncouple option. (I hope that makes sense.)
