The board can be stacked or even in the same plane as long as the connections in the break away section are still wired together. They have doubled the holes there for that reason, to be use with headers or ribbon connectors. For the ultimate small HP, at the sacrifice of depth, you could put both boards on the same plane with the midi board behind the main one.
The next size is the main board horizontal making a ~23HP panel, with the MIDI board stacked above or below it. That would leave a lot of room for controls and jacks too.