For what its worth, I have a custom fender installation to fit under the rack. Basically, 2 fenders cut and bolted on the rack; one normal one going from the front of the wheel up to the rack; cut and trimmed nicely for a good job, and then a mountain-bike style fender going out the back.

The photo sucks as I took it with the bike on the rack :-) but it gives an idea. The difference between the 2 fenders is really made obvious in the photo because of the shot angle in the flash. In reality, its hardly noticeable.

It was the idea of a creative young fellow at the bike shop :-) I've had this setup for 7 years now