I have the BMW base support system, so factory crossbars. I used 2 different Thule boxes on them without any problems. The factory crossbars are definitely a larger diameter, so I could easily see issues with their size and certain accessories. But have not had any issues so far.
I too have heard that the factory system is relabeled Thule though. Also, you can usually pick up a set on the forums for much less than what you quoted above. I got mine on here for $150 with everything.
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