Had to delete Locations.cfg which came with mod as caused CTD (calls up bits and bobs that I don't have).
Edited my Locations.cfg as suggested, and all ran OK.
Nice model
The base extended beneath the surface of the sea (although placed using locations.cfg). I can confirm that it was solid when I tried to drive through) and that the light was not visible when it was behind another object.
I played around with settings in Gap's reef model (hope he doesn'tmind?). I found that by giving the Node-Reef1 Node Positioning Translation Y value a negative number (here -30 see 2nd screenshot) the model did go beneath the sea (see 1st screenshot of underwater view of sub)
I also tried changing the StaticObject parameters and setup to reflect yours but the boat still drove through.
Hope this helps.
All reminds me of this:-