Essentially, he's making a hole in the hitbox of the ship, that smaller craft can fly into, and the docking bays open when the carrier itself releases an item, much like in vanilla.
The idea is pure genius actually. Kudos, Tink.
As for the ship being too much, naturally, how about it'll only be sold in the main home system of the house? As in, used mostly for defense and such and such? Naturally, because it'll only be able to dock on planets, and not jump gates. Just an idea.