-- Last Updated: Oct-11-12 3:25 PM EST --
There's a guy in my town who transports a long, fragile racing canoe on a small, four-door sedan using an extended rack system. Basically, attachment points on the roof carry a special rack which supports two lengthwise bars, one on each side. That pair of lengthwise bars carries the actual crossbars which in turn carry the boat. Thus, the rack is a two-stage contraption - a rack which supports a rack. The front crossbar is about 4 or 5 feet in front of the windshield and the rear crossbar is about as far back as the car's rear bumper, or maybe a little farther. Total spread between the crossbars is around 8 or 10 feet. I think there are two pairs of diagonal struts which stiffen the lengthwise bars against side-to-side flexing.
Wind pressure against a long boat puts much greater stress on your rack-to-roof connections than what happens with a short boat, so those connections must be very secure. Using this super-long rack system does not change stress applied to the roof (assuming that the boat is securely fastened to the rack regardless of what amount of bar spread you have), but what it DOES do is reduce the stress on the boat itself, since stress occurring at the boat-to-rack connection points is much less when there's a lot of spread between the crossbars.
If it were me, I'd build one of these extended racks. It could be built right onto an existing rack. However, the one I've seen carrying the racing canoe is obviously commercially made, but I can't tell if it's Thule, Yakima, or something else. I'm sure a search would turn up something.