While I don't have much of an answer for you regarding future development of the sort you're asking about, I do think I know how you can get your deck gun crewable once again. This same bug has occured to me twice, each time when my boat was refitted. Like you, the aft deck gun was replaced by the game with a bow-mount, and the first time I didn't know how to fix it, so like you I made do. That career was also affected by the Terrible T problem and I got time warped back to mid '42, but I digress. In your TMO folder you will find a Documentation folder, and inside it is an optional mods folder with several optional mods for the...mod, heh

Look for the TMO_Aft_deckgun mod, and copy it, then paste it into the mods folder along with all your others. You can activate it while you are in port and your deck gun can go back aft where it belongs, and will be crewable once again.
While I am not using the RSRDC mod yet, my mod-list is very nearly the same as yours, I activated the deckgun mod after the small patch, put OTC on top of that, and the ISE on last as you did. Everything works just fine, so you shouldn't have any issues caused by adding that mod to fix your deckgun problem.
EDIT: A thought came to mind shortly after I posted this. You may find some useful information pertaining to your question in the TMO manual Ducimus wrote for the mod, including new equipement for the American boats as well as useful info regarding increasing capabilities of the enemy ASW craft. Its in Pdf format, located in the documentation folder of the mod.