Solution to the problem in the first post:
It's exactly as rowi58 said - the compass was not centered... not in Turm7c_1_hd.dat, but in Turm7c_8_hd.dat
At first I've found similar turm in Turm7c_5_hd.dat, so I've fixed it there, but it didn't help. I didn't know that the game is using three files (Turm7c_1_hd.dat, Turm7c_5_hd.dat, Turm7c_8_hd.dat) for one turm
I didn't know how to center the 3d model in wings3d, so I've just exported the good, centered model from Turm7c_1_hd.dat, imported it in Turm7c_8_hd.dat, and copied the node positioning from the good compass.
The good thing is, that I know now how to repair it. The bad - I cannot share it because of the size of the files and as I see, the GWX external compassed are broken in this aspect, so it's a fix that must be repeated with change of u-boat type.