From the couple weeks that I've had the aluminum bottom, I haven't seen anything that would suggest that the aluminum will fall apart faster than the steel (should even outlast it since it won't rust). The cross member beams are galvanized (sp?) steel just like the steel rack, so both are supported the same. I suppose if you put something very heavy at the ends, you run the risk of bending the aluminum bars, but that better be something extremely heavy and small. If you are putting a tire up top, the tire will be supported by the cross member rail which can easily take the weight.
Philosopher is right about the gas mileage though (I haven't noticed an acceleration drop much). I think I've lost about 1 MPG since adding the roof rack.