The idea of locking aperture seems appropriate if you shoot with a dome port. For example on the 7-14mm I would not go below f/5.6 however with a wet lens on a flat port do you really need to do that? Are you not better off working in S mode with fixed shutter speed and let the camera work things out.
If your camera is not moving like a close up or a fixed position wide angle shot then I can agree that manual is fine and there are no real issues like taking a still image net of movement in the frame
The IRE question on water column is interesting. I guess for shots with light the water colour will be pretty much dictated by your main subject and the shutter rule. So if you shoot at 24/25p your shutter will be 1/50 and you will get a lighter blue than if you shot double frame rate 1/100 or 1/125
For ambient light I do not know really if this concept holds as you set IRE on your subject as you say you do on land and then try to avoid clipping. Generally IRE for broadcast are 10-90% for safety so you need to be careful to underexpose too much or shadows would be gone, this is where filters come helpful as they act only on certain wave not all of it. A filter takes away one stop from the image in general but only from the blue so your water column becomes more pleasing and generates more perceived contrast. White balance a grey card or similar does not have the same effect of a filter and you get an image that has less saturation and less contrast so if the blue is a bit washed out it stays so afterwards. Filters tend to introduce hues so when combined with white balance it works best. This is however a long debate filter no filter and not generally connected with getting the right exposure!