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I don't believe the weight restrictions have anything to do with the ability of the crossbars or the roof to support the weight. I believe it has more to do with the vehicle's stability. The more weight you have on the top, the more 'top heavy' it becomes, affecting the stability of the vehicle, especially when turning. The weight of the moonroof is taken into account and results in a lower 'carrying weight'. Also, the weight will increase with speed as well.
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Peter