I have trouble with my NV and the 800mm+ wide handle bars (uncut Sixc) on my downhill bike when it's in the closest tray, but that's where loading order or the sliding rear glass comes in.
Bikes are my number one passion, so I'll share how I use my rack, and my experiences with different racks...
How random, I'm pretty sure saw you driving a few days ago, can't be to many red T4R with black hoods rolling around Denver. Truck looks good. Disappointed to hear about your trouble with the Toytec setup as I was ready to go with the Boss CO
I have the Thule Aeroblades on my T4R and have had the Yakima Whisbars on my Golf R, neither made noise. It's the people that get square bars and hang them a couple feet off either side that have issues with noise. The aero type bars also look way better since they adjust to the rack width...