This is a great way to reconcile FJ's stuff with later trek tech, especially when one considers that, with this design interpretation, science probes could also be launched from this location, which makes sense since the superstructure is the main science labs area of the ship after all. Keep up the great work!
P.S. Have you given any thought to what's inside the torpedo casings? Perhaps one or more spherical anti-matter charges, like that seen in "Obsession", sits in there "egg-carton style" for variable yield torps, this would also segue nicely with the idea that the photon grenades from "Arena" are smaller versions of same? Anywho just a thought, carry on.