I think that the problem here is not being clear about what a shot is about. Many underwater photographers equate much underwater photography with natural history photography in which case the guidance for manipulation is well established - nothing which changes the 'essential truth' of the situation/image is allowable (and this is still subject to discussion!). But for other aspects or types of photography manipulation may be acceptable or even needed. The RPS nature group has an excellent code of conduct for nature photographers (I have a printed copy but can't find it online) the gist of which is that if you have to disturb the subject to photograph it then don't take the photo. Of course underwater photography is a little odd in that disturbance is almost inevitable given our size and need for life support systems. And if disturbance is required to take a specific shot for a specific purpose (I've moved two starfish - Luidia ciliaris and sarsi, closer for illustrate their differences for ID purposes) then the shot may be classed as technical or scientific but isn't natural histrory and shouldn't be classed as such.
Some types of (non-natural history) photographs still portray 'reality' (documentary for example) so obviously manipulation is still out, others want to portray a specific idea so more or less anything is acceptable (advertising). But to manipulate a scene or image and claim it to be natural is unacceptable. Conservation is of course an entirely seperate topic and whilst I'd like to believe that all underwater photographers are conservationists I know that it is simply not true.