No, the crossbar wont go any further forward with the Thule setup. It raises the whole box at least 2"-3" higher.

Look at Pac2006 's picture, you can see if it was any lower, the rear hatch would hit the Cargo box.

Moving the mount location of the cargo box forward to clear the hatch would cause the front of the cargo box to come in contact with the roof, which is why I mentioned going with spacers and reinforcing the bottom of the cargo box to prevent it from warping from wind pressure, if needed.
I'm just going with a stubby Thule Box with stock crossbars, it should clear just fine, front and rear.