I don't know if this a complete bug or not. The assault transport can land in many case the same way a normal fighter can land, which is fine. But when I tried landing on Battleship Myoko, it tried landing through the path like a normal fighter. It went into the normal docking screen and tried to enter the battleship, it did nothing but bounce while trying to enter. It may happen to all battleship of this design, but this is the one I ran into.
I've encountered a similar glitch while trying to dock in an Order Bomber onto an Osiris, but its easy to get around.
You will always dock at the closest available port that is closest to your ship when you request to dock, simply move to its mooring point, the KU BSs moor point is at the very front of the ship.