It's true that you can focus very close with the 12-50 in macro mode, but if you want a bit wider picture, so you go into non-macro mode, min focusing distance is long.
I don't get significant extra macro from a +6 diopter on the 12-50, and I believe that is what Phil reported also.
I think these two lenses serve different purposes despite their overlapping focal lengths. The 12-50 in the Nauti dedicated port is more of an "all around" lens. It is a very capable macro lens in its own right without any attachments when placed into macro mode. With the new super-macro diopter combined with macro mode it is really something. It is also a good semi-wide to moderate zoom in normal mode. But, in normal mode, it is not as versatile at the 12-40 for
wide angle work because the Nauti port is flat, optimized for macro.
The 12-40 is faster, and, behind a dome, wider. It offers more versatility for big animals at a distance, and also for scenics and the fast aperture gives more exposure flexibility in those arenas. But, behind the dome, its close focusing distance is going to be impaired even for its only semi-macro close focus, due to the dome sticking out and cutting off most of the working distance and, of course diopters are not really viable.
Thus, if your dive will put you on tiny macro critters, beautiful reefs, larger fish portraits, and everything except really big animals all on the same dive (the 12-50 is just fine for turles, dolphins, most sharks but not huge things), the 12-50 is the best bet as it will be very useful for all of those subjects. Also, if you don't know what to expect, the 12-50 covers more potential subjects.
If you dive is dedicated to semi-wide scenics, larger fish or animals at a distance, or shooting models, the 12-40 behind a dome would be a better choice.
The ideal set: a dome for the 7-14 and 12-40 lenses, and the 12-50 dedicated port for the 12-50 and 60mm macro. There is nothing you couldn't cover with those two ports.