Originally Posted by Randaddy
You should talk to the Toyota dealer and find out if there's a rack designed specifically for your car. I found the Volkswagen brand rack for my Jetta on eBay for $130 and it's beefier than a Yak or Thule. It also attaches with an included torque wrench to bolts in the rain gutter. Basically, I got the factory rack and it's much higher quality than the after market racks.
I find it amusing that you knock Thule while celebrating their "factory" racks!
I had one of them for my Saab 9-3 and thought it was awesome. The Saab catalog even listed both the square bars and the aero bars, like your VW has. That car had the same threads in the roof, and the towers had allen key bolts in the base that went into those threads. All in, it was pretty bomber.
OP - in regards to your Toyota, these guys haven't figured things out like the Germans (I'm calling that Saab German on the basis of it being 80% Opel) have. You'll likely have to use that system that puts an appropriately shaped rubber pad on the roof and a clamping arm in between the door and frame. It is important to get these on right: watch for imbalance of the loading force between left and right, and watch to make sure the bar is square. These two things will help those rubber pads make maximum contact, preventing the rack from peeling off the car at speed. Thule and Yakima use the same basic thinking here.
Keep in mind that 4 kayaks on the rack at speed represent at least as much aero drag as the car itself, and remember that all that force has to go through your towers.
Finally, a trick for you: find an old mountain bike tire, and cut out the tread into kind of a shed snake skin shape. Zip tie this to your bars. The bars are finished with a slippery engineering plastic, as is your kayak. The tire will make the bar non-slip, preventing you from making a massive dent in the side of your car like most other kayakers.