I've run into this problem myself. But I'm not a big fan of racks that grab the downtube of a bike -- it can be difficult to adjust the clamp just right -- too tight and you damage the bike, too loose and the bike moves around and gets damaged anyhow.
One rooftop carrier that I've seen does away with the full-length wheel tray -- made by Yakima, called the Boa: http://www.yakima.com/
For other rooftop carriers, there are adapting devices that you can buy that attach to the front part of the bike rack where the forks attach -- these devices raise the front fork a couple of inches, giving some clearance for the fenders. However, some of these are designed for mountain bikes that have oversized axles and disk brakes (the disk brake mounts create clearance issues, too). I'm not positive if the dimensions for some of these are the same as for a typical road bike fork, so check the measurements before you buy one. One thing that bothers me is that these devices tend to be pretty expensive for what they are.
There are homemade options as well. I built an adapting device similar to the ones I just described -- using some 1/4 inch aluminum bar stock, steel threaded rod, and an old hub axle. It may also be possible to alter a carrier with a full-length wheel tray so that it looks/works a little more like that Yakima Boa design.
One other rooftop carrier I've seen would work -- it is designed primarily for tandem bikes, but it is a "telescoping" design that works for single bikes as well. It's a pretty expensive option, but if you happen to also own a tandem, it would be worthwhile. It is made by Rocky Mounts: http://www.treefortbikes.com/
Kyle Brooks Akron, OH
To: classicrendezvous@bikelist.org Sent: Friday, August 7, 2009 3:42:17 PM Subject: [CR] Best Roof rack for fendered bikes?
Dear List:
It seems more and more of my bikes (all on topic, of course) are sporting fenders these days, and with that comes the problem of carrying them on the car. You can't throw them in the back of the minivan with a wheel off, as the front fender impedes storage, keeping you from turning the handlebars 9 degrees. You can't put them on a fork mount roof rack, because again, the front fender hits the wheel tray. You can put them on a trunk rack, but it's harder to lock them for a quick dash to the store while driving to the ride start.
So I'm seeking advice for functional roof rack carriers that will be fender compatible. I suspect it will have to be one that leaves both wheels on, but grabs the down tube, not the front wheel. In particular, I'm looking at the Thule Big Mouth. (I have both Yakima and Thule bars, so a carrier that works with both is ideal.) My only concern would be water bottle cage interference where the carrier grabs the down tube. Is anyone using the Big Mouth with a fendered bike? Any pitfalls to watch out for? I'd be interested in any other recommendations or alternate solutions. What say you, group?
Tom Adams
Manhattan, KS USA