Im working on a solution for this issue for PE4 and have find a solution to the problem, which is out for testing at the moment so that we can have both the ROW sub and roll pitch mod and a submarine that sits deeper in the ocean, for more information see this thread:
http://www.subsim.com/radioroom/showthread.php?t=138663
So far the feedback I have received have been good, including feedback from a guy who actually sailed in a Balao class submarine during WW2.