I thought I'd answer my own post for anyone else that has a similar question...
I ended up with a Thule Force M cargo box for my Venza ('13, LE AWD - factory rails and bars). The box fits without hitting the rear hatch spoiler AND without mashing down the vehicle's antenna. The one sticking point I have is getting the box on the car - mostly good except that the attachment system Thule utilizes (adjustable clamps, like claws) initially hits the roof when the box is mounted. Once the clamps are locked down to the crossbars, this isn't an issue. I think the best thing to do to avoid any paint issues because if this is to place a towel or something on the car's roof when mounting the box, then remove once the box is tight to the vehicle.
We have a Yakima rack and box that we used for camping once. Can't use the sunroof and the Venza has provisions in the frame to allow for the rack placement. Check out my thread for a idea with the rack alone. I don't have any with the box though. No problems with the antennae.
It did happen, I swear! I'll try to get some pics up at some point.
The cost was about $340 (for the box); store was running a 20% off Thule stuff - car came with factory rails/bars when I bought so no cost there. I wish Toyota would have set the cross bars up a little higher off of the rooftop...anyone know if you can remove the factory bars (I know they come off) and replace with Thule or Yakima crossbars that sit up a bit higher? It looks like the factory cross bars are set in to the factory rails so I'm wondering if this was done...would there be any issues?