Another plus for the thule/yakima base with a basket (homemade or store bought) is that you can pull the basket off and just use the rails for what every you need.
I also have my basket mounts under the bars with u-bolts rather than over - it only sits about 1" over the roof at the closest point. With the fairing I have not experienced any mpg impact, and that is even with ski racks up top.