As between the 12-50 and 12-40 I am staying with the 12-50. Like Phil said, the 12-40 is best suited to (1) large subjects like larger fish portraits at a distance, divers, and semi-wide scenics or (2) available light photography without flash where the larger aperture might help, or (3) fill flash photography with the highest sync speeds (think, models in a pool). The useability of the 1:3 magnification is highly questionable underwater because of the big dome plus extensions. The glass will be right up on the subject. I would not expect much macro use out of the lens because of that. The dome is mandatory due to the very long lens physical extension during zooming, so no flat port for macro use is even an option.
The 12-50 serves a different purpose. It is the "do anything instantly" lens. Even in the flat port, it has decent wide angle coverage. Its macro capabilities are far superior to the 12-40 and the Nauti port-gear makes it instantly accessible (with the port also holding the 60 macro as well). Personally, I also shoot video underwater sometimes, and like the power zoom. YMMV. I can best illustrate with an experience. A night shore dive in Florida. Out on the reef, in macro mode, getting shots of flamingo tongues. A turtle swims by, in three seconds I am shooting wide angle turtle shots and then face portraits. The turtle is swimming fast and so am I and I have to kick hard for quite a while to keep up. The compact port is a real boon here (or in a strong current on a reef drift when you have to stop in the current for a shot). This scenario never could have happened with the 12-40 behind a big dome.
So, consider what you want in a semi-wide zoom and choose accordingly. Don't let obsessive internet pixel-peeping over lens quality drive the choice because many other things are even more important, like getting the shot!
Also, the image quality differences might not be that great in normal use. For most u/w shooting, especially with flash and macro, you are shooting small apertures. All lenses tend to get closer in image quality at smaller apertures. There will not be a decisive difference in the image quality of the lenses for most underwater shooting. I have never seen a file from my 12-50 that would not make an excellent large print or be perfectly publishable at magazine scale.
For wide, I use the 7-14 behind the nauti 6" dome for that lens. Still nice and compact. the 8mm fisheye even more compact.
The 12-40 is king on land due to quality and speed, but not so much underwater where versatility tips to the 12-50. I have a 12-40 on order, but it is not going underwater. I am keeping my 12-50 permanently encased in its gear and dedicating it to underwater.