I wired my lights through the roof rack bar over the drivers door. I had to drill another hole, but at least it is not a hole 3 inches from the roof rack bracket like the TRD instructions say.
I'm pretty sure I drilled the hole between the two stock bracket mount bolts (underneath the plastic bracket and rubber seal. You will need to remove all the roof rack bracket bolts on the driver side so that you can lift the roof rack up enough to drill the new hole. Then pull your wires into the headliner area and down the inside of the A-pillar. Topside, you can drill a new hole on the inboard side of your main roof rack bar (driver side) and fish the wires up through the headliner, bracket, aluminum tube and then nothing is exposed. IIRC, I had to drill a hole in the plastic bracket and cut a hole in the rubber seal to fish the wires up the tubing. Sorry, it's been too long since I did the install and I didn't photograph the process.