So is there an advantage (disadvantage?) to using a Macro lens behind a dome?
Advantages:
* Wider angle of view. This means at the same distance from port to subject you can get more in. This will be useful for larger subjects. For the same subject area covered the distance from port to subject will be smaller, i.e. less water. All this means you have a wider range of possible subjects at the larger end of the scale.
* It may be possible to share the port with other lenses, such as zoom lenses so if space is a premium, you can reduce the number of ports. I can use the same dome port for my 60mm as for my 18-55mm zoom.
Disadvantages:
* As you get closer to 1:1, the distance from port to subject is greatly reduced which makes lighting more difficult. i.e. is there enough gap between the edge of the port and the subject to get the strobes in. Even if you can get the light in, it may all be coming from the side rather than the front of the subject
* Another medium through which light must pass - see below
Adding a diopter is obviously another element which will affect cost/clarity/light/??? and thus seems bad.
This is true, in theory. In my experience, however, the optical quality of the diopter is better than the dome port and has less impact that the affects of the water itself. For me, there is no obvious loss in quality but the advantages are valuable.
To answer one question raised, I typically dive in clear warm waters where 6" of visibility is not a problem. And I shoot critters that dont want me to be 10cm away... sometimes. I would like to take pix of Octos and Nudies, (and obviously the more exotic critters of those sizes/personailities) and the occasional reefscape.
Nudibranchs can be taken equally well with either the dome (and +4 diopter) or the flat port, unless they are very small, in which case the flat port will excel because of the greater distance to the subject. Here is an uncropped nudibranch photograph taken with the 60mm in a dome port with a +4 diopter:

Octopus photographs may be difficult with either lens because you need to move further away. I think for this, the dome port and +4 will work slightly better. Here's a shot (uncropped) from the same dive as the nudibranch above:

I can even take fish photographs with the dome port and +4 diopter:

Also there are big ranges in dome sizes... 6" - 9+". I imagine the advantage of bigger dome is the light entry point is further from the lens so the virtual image is further from the lens and thus reduces the need (or power of) the diopter. I expect the higher power the diopter the worse (although I presume it is imperceptible anyway) the distortion.
I don't have a huge experience with dome ports so I may not be the best person to answer. I believe larger dome ports are more important for wide angle lenses and I doubt you'd get much advantage, if any, putting a 60mm lens in a 8 or 9" dome port over a 6" one. Adding a diopter (even for wide angle lenses) is often recommended to REDUCE edge distortion and +4 is meant to be better than a +2. I believe a larger dome port results in less distortion but I don't think this has anything to do with the use of a diopter or not.
There are also various flat ports by the same manufacturer... for example I am looking at a Sea & Sea housing. They list several flat ports but the one they say is for the Nikon 60mm is the Custom Flat port. Is this just because that is the size of flat port that accomodates that lens... I imagine so. And then presumably it is fat enough for the 105mm and I would just add extensions...
You need a port that is wide enough and long enough to accommodate the lens. You don't want the flat port to be much longer than the lens at full extension as you may get vignetting.
For the WA, they recommend their NX FishEye Dome Port, and then an extension ring... this dome says it is made specifically for WA...
The dome port you use for wide angle depends on the length being used and I don't think you can recommend a "one port fits all".