Here is a couple of options for storage on your Highlander.
I bought all of this stuff off Craigslist locally. This is a great way to get your stuff cheap!!! I got all of this stuff for about 80% off MSRP.
This is a Thule setup. The crossbars are 50 inches mounted on the Crossroad 450 mounts. The box is a Cascade 17 with 2 basic bike trays on either side. The rear box is a Thule Transporter which has a 4 pin brake light setup.
I highly recommend the Thule crossbar setup. It feels welded to the roof, with zero flex. The Cascade box is not properly fit for the car, but I was able modify the box. I had to make 4 new holes to move the box forward to allow the tailgate to fully open. It took all of 5 minutes to do. There is no movement of the box at highway speeds and very little wind noise. The bikes make a bit of noise though.
The rear box is very sturdy as well and much more accessible. It has less storage than the roof box, but its dimensions will hold some larger objects.
Keep an eye on Craigslist and modify a box if you have to. There is tons of stuff like this. You don't have to buy a new Atlantis box for $500 plus a $250 rack system.
Maybe I should have bought a bigger car.... I don't use both boxes at same time - these are illustration pictures only...