In general, a manufacturer's roof rack will be of high to excellent quality and will completely fit the vehicle for which it is intended. However, there may be constraints on the number of accessories available for transporting specific loads. This could include bikes, skis, or surfboards, for example. Also, in many cases car manufacturer’s roof bars rely on a tool for security and not the more secure options of physical keys and locks. Bear in mind also that most roof bars from car manufacturers are designed to fit a specific car model. The case for proprietary brands, such as Thule roof bars, is that they are generally of equal, if not better quality, and in some circumstances, but not all, may be converted to fit another vehicle.
Car manufacturers rarely build their own roof bars, instead relying on major brands and having the bars and fittings custom-made to suit the vehicle. Because a manufacturer's roof bars are generally created specifically for the car, they can appear neater, with shorter fitted bars. However, this can also be inconvenient if you need to transport large or multiple goods, such as several bike racks or a roof box and bike racks.
In conclusion there is no right or wrong decision to be made. Whether you choose roof bars for your car from the vehicle manufacturer or obtain a bespoke system from a well known reputable roof rack manufacturer such as Thule. However, always make sure that the indicated loading capacity for the roof bars and for the vehicle is adequate to support the weight of the load you intend to transport.
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