if you will note in this picture:
I have included a "pass through" to the deck above the torpedo bays that is definitively inside the neck. Certainly I could have implemented this as a single bay with a deck above, but we have a clear indication in TWOK that there are two bays. My choice is either to make one bay, or to make the two bays smaller than seen. Neither is a great choice. I said all along that some things just were not going to fit as seen on screen. If you can figure out a way to make it fit, more power to you. This is the compromise I made. Others could be made. A logical design would have been yet a third (or fourth) option. Certainly the design as seen in TWOK is not as efficient a design as it could have been.