The merge block is not a good tool to use for docking. The very fact that it merges and splits grids (which is exactly what they're supposed to do) makes it a pain to use in conjunction with scripting because it's difficult to separate blocks per ship. However, we do have pressurization, one of the more interesting features of the game.
I would very much like to see a docking collar system that works more like the connector. Creating an airtight seal, but does _not_ merge the grids.