Your Scoob is a 2006 and not a 2001. In 2001, the OE roof bars sucked donkey balls, and were nothing more than something to be thrown out. The locks failed almost immediately and the tensioning mechanism breaks right after that. Junk.
To each their own, but the thought of three or more pairs of precious Dynafit bindings being exposed to flying road grime (including the rocks that Alberta thinks is sand, as well as the copious amounts of salt that no one in Alberta admits we use) makes me ill, so inside a box is a must for me. I drop the rear seat and put them inside the car whenever possible, but the reality of backcountry skiing is that you need partners, so we typically have no vacant seats, so inside the box is where they go.