Replace the factory racks and install the yakama rack system towards the center of the roof. I had no problems removing the oem racks. I have an 09 AWD with the factory racks. This does not affect your car warranty and is against Canadian Consumer laws (can't recall which law it is).
Look at the picture matrix photo gallery with yakima roof racks on it, that is my car.
If you take the whole roof rack assembly, you will have to get the plastic clips from a GM dealership, because it is cheaper or search around an auto wrecker if they have any damage 2nd generation Matrices on the lot. And also get the molding because underneath the large 2 rack holders there is no molding underneath it. Net a flat tip screwdriver to pop off the caps, allen wrenches and socket wrenches to remove the whole entire factory racks.
Aftermarket stuff will look stupid if it is backwards on the factory racks and it would damage your spoiler if you open the back hatch if you put it normally forwards. Putting it backwards would not damage the rear door and the spoiler.
If you have any issue, just go to a rack shop and they would gladly help you. Remember you might have to buy new towers or replace the clips if the towers can fit and a flaring if you have the same size recommended, if not replace it.
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Roof Rack: Factory or Aftermarket?