Today I modified my basic.cfg file to edit the ammunition type and quantity for both deck guns. My modified file looks as follows:
[AMMO_TYPE0];10.5cm SK C/32
Idx=0
Year=1939
Month=1
AP=0
HE=150
SS=0
Renown=0
[AMMO_TYPE1];8.8cm SK C/35
Idx=1
Year=1939
Month=1
AP=0
HE=220
SS=0
Renown=0
When I told the crew to man the deck gun, the crew manned the weapon without any round loaded in the chamber. To get the crew to load the round, I clicked on the HE shell and, sure enough, they started to load the first shell.

I think this is a pretty significant finding, since one of the main points of contention with the RuB deck gun issue is that the default game does not factor in the time to prepare the gun for firing.
In other findings, I made the following change to the FUMO-29 radar setting:
[EQUIP4]; Radar
DaysSpent=2
Nb=5
NameIdx0=1275
Year0=1942
Month0=2
NbSub0=2
Sub01=2;IX
Renown0=250
Name01=FuMO29GEMA_type9
This keeps the Type VII U-boats from having access to this type of radar, as 3 type IX boats (technically all IXCs) were the only ones to use it.
Lastly, I wanted to change the configuration of the 2cm AA guns so that they carry only anti-aircraft ammunition, but I was unsuccessful in doing so. Has anyone else tried this and find it to work?