I got a BMW factory roof rack a couple years ago
(link to pictures/info) and finally pulled the trigger on a nice Thule Ascent 1100 roof cargo box. Got a great deal on Craigslist
I was always wondering if the Thule box clamps would fit around the big chunky BMW loads bars. It turns out they barely do, at least not enough for me to be comfortable with the fit. My plan was to buy two 6061 square aluminum tubes (1" to 1.5" range) and make my own. But then in my frequent browsing in the REI Scratch and Dent section, I came across a pair of 47" Thule Aero Bars for $35. They are $125 normally! That's about what I was going to pay for raw, square aluminum tubes so I thought I'd try to make them work. From my browsing in the store I could tell the attachment system is similar to the BMW bars (also made by Thule I belive) but not the same. I thought I'd need to do some significant modification, maybe even take it to a machine shop for some light work, but it turns out they work great with just a tiny modification!
Here's the problem with the factory bars. The box just barely grabs the bar.
The slight modification involves grinding the steel threaded insert that slides in the load bar channel by just about 1mm.
You can see how it slides into the Aero bar channel.
Simply bolt it down tight and that's it!