Now that I've gathered my thoughts....
A dome port will always reduce chromatic aberation. In a perfect world, we would use a coated optical glass dome port designed for each lens. In fact, Seacam offers 3 different dome ports maximized for various wide angle lenses. I have met adherants to the dome port for everything mentality. I believe the advantage is more theoretical than practical. Kind of like the guy who "proved" to me that one print was better than another by looking at it with a 10x loupe. There is no chromatic aberation with a 60mm lens. The light just doesn't get bent that much. Chromatic aberation rears its ugly head with wide angle lens, especially poorly constructed ones. That's one of the reasons we use dome ports for heavily curved wide angle lenses. No other housing manufacturer other than Ikelite even lists a dome port for a macro lens even though it's possible to do so. Why? Hold that thought.
If I were to magically stretch the focal length of a lens, then it would require more light as our effective f/stop would increase. But this is not the case of the 60mm and 105mm. The design of the lenses are different. They are both 2.8 lenses and allow for the same amount of light. If different focal lengths affected light requirement, then all our hand held light meters would be worthless. The longer the lense the more difficult to "equalize" this light requirement, or should I say increase aperture size to get the equivalent light through the lens. That's why my 200mm macro is an f/4 as are many telephotos.
This of course does not apply to lengthening the lens with a TC or tube. My 2X TC loses 2 stops of light. Even so, I'm able to do macro with the TC and 105mm at f/22 and get enough light from my strobes.
"The 60mm allows me to get closer" should be "The 60mm allows me to backup less to get a non-macro shot". With its smaller angle of view, the 60mm allows you get larger subjects totally inside the frame. For true macro work, it is not as effective as the 105mm. The 60mm does 1:1 at 8.75". This is the distance from film plane/CCD to subject. Now add on the space of the dome and it gets very difficult to get that close to subject. If you are using an 8" dome, it really gets hairy. You are almost in framer territory. Hence, the reason flat ports are recommended for macro work.
My revised final thoughts:
60mm - More versatile, easier to shoot non-macro fish portraits. The image crop of the S2 makes this the best overall choice. It is also a much more practical lens on land.
105mm - My personal choice. I can still get full fish/octopus shots with no problems and get the extra working distance for macro. I've even used it combination with a 2x TC or diopters for even greater magnification. I look forward to using it with the D100 for easier macro work, but it will lessen its versatility for non-macro work.
200mm - Forget about it. I love this lens, but underwater it is a royal pain. It has allowed me to get some shots of skittish critters that I couldn't get with the 105mm. I won't detail all the pitfalls, but suffice it to say it requires lots of strobe power and a tripod would be extremely useful. Great for eyeballs.
One last shot; Ikelite dome ports are, in my opinion, the worst optical quality dome in the market. They were designed to meet a cost target. They only come in 6" versions, which are not optimized for really wide lenses. It may not be a factor with a macro lens, but I would always shoot my macros with a flat port.