I'm not sure if it voids the warranty, but here are two ways I did it or a rubber boot you can use for varying number of wires. Yes, it's on the driver's side where the main wire loom enters the FJ. You can see a portion of it in the photo below on the bottom edge. It's easy to pass wires, you just have to cut the firewall insulation. I cut it first, then drilled. I only cut 3 sides of it to create a flap so it's still attached.
The smaller cable gland uses an exisiting hole I enlarged and the larger cable gland is a new hole I drilled, both with a step down bit.