I have mine run out through the rear hatch grommet and then up to the roof. It was fine in the place you describe until I put my custom rack and tire up there. That blocked the signal a few times in certain directions. I moved it further up and actually mounted the magnet on the spin down I have securing the top of the tire.
The wire runs through the grommet, then inside near the tailight assy staying behind the molding. Then under the carpet, under the seat cushion, under the carpet and up at the center console where I have my Sirus receiver installed.
_________________________
My X2003, 3" SL, 2" BL, 33"x11.50 BFG KM2's, 1.25" spacers, Shrockworks sliders & bumper, custom rack, Warn 8K, etc
HigherGround4x4.com