Yes, it is perfectly possible to use a 100mm macro lens behind a dome port. If you are using the 100mm usm lens from Canon its simply a matter of ensuring that it fits - so you will need to see if and which extension tube you need. I tried out the 100mm usm macro behind Seacam's DP95 and PVL35 Extension tube recently in Tahiti. On the dive I found that I could shoot small clown fish (now called 'Nemos' I'm told!) with no problem and the results are certainly sharp enough. You still need to adjust for a slight amount of chromatic fringes during the raw conversion, but differently to the adjustments needed for a flat port. You will need to shoot at f/11 or f/16 so any non-flatness of the image will not be noticable. My only concern is the one already mentioned - it would be very easy for the Superdome to physically contact the subject, so there is a risk that you could damage either dome or subject.
If Paul says he has had good luck using the 100mm macro behind a dome port, I believe him. But, there is a wild card. He used it behind a DP95, and you want to use it behind a fisheye port. The issue is that the minimum focus of the 100mm macro is 12 inches. IF the dome has sufficient diameter to allow the vitual image to appear 12 inches or FARTHER, it will focus. If the dome creates a virtual image NEARER than 12 inches, the lens won't focus at all (unless you add a diopter).
So, even though the 100mm macro focuses to 1:1, it does so at a dstance too great for the use of some dome ports. Yes, you would be able to use the superdome (9" diameter ... approx. 18" virtual image) with the proper port extension, although why would you? Maybe the DP95 uses a similar curvature dome, although in a smaller package. That one I can't answer without further research. But, I can guarantee that if you try using a 100mm Canon macro or a 105mm Micro-Nikkor behind a 5" dome (approx. 10" for the virtual image), you won't be able to achieve focus without an accessory close-up lens.
BTW, I have done a pool test with the fisheye port and 100 macro, for much the same reason as you, I wanted to travel somewhere with fewer ports. It would not focus. You could buy a diopter for your lens and no doubt you could make it work, but unless you can focus on the virtual image of the fisheye port, I think you'll be very disappointed. It is very close to being able to work I think, but still off. There is a romote possibility that working at F-22 might give you enough depth of field to catch the virtual image, but I surely wouldn't go on location counting on it.
While we are on the subject of macro lenses and domes, I have often used my 50 or 60mm macro lenses behind my fisheye dome. The reason being I wanted to be able to get close to medium sized fish and still get the whole fish, not a head shot like the refraction of a flat port might render. However, I don't believe I've ever been able to get 1:1 with my 50mm Sigma macro behind that dome, and I think it is because minimum focus happens at a point inside the port.
Just speculation on that point, but I know I can't get the same 1:1 magnification I would get with a flat port. I'm interested to know if Paul was able to get 1:1 with his 100 macro/DP95 combination. Paul ... did it focus through the whole range behind a dome port? I know you said you got clownfish, but did you try to shoot really small critters too?
Anyway, for so many reasons, you really need a flat port with your Seacam and 100mm macro, not the least of which is the ability to add the Wet Two diopter. http://www.seacamusa.com/wet-two-diopter.shtml