I had a look into the aix files and I think your modifications wont have any adverse effect on other conning towers. As far as I can understand, we should had two new crew memebers if we want if we want both Vierlings to have two men (0n for elevation, on for training) on them.
I also think I have found where slot values selectable in GunStationControllerProperties are stored (that's init.aix). If that was true, we could probably add two more gun bones to the conning tower GR2 files, usaful for equipping the U-FlaK with two additional 20 mm guns through upgrades menu. Manning them with visible AI crew, whould require the addition of two more crew memebers though.