I'll add another option, how about a bed mount system? I have a Yakima Bedrider, which mounts to the bed sides. Takes about 5 minutes to take off should you need the top space, otherwise I just leave mine there, allows easy access to bikes or whatever, not too tall while allowing the use of your hitch or tailgate when a bike is mounted.
I also have an aversion to roof mounted racks since the truck is so tall, imagine adding a bike on top of that. Then there is the fear of forgetting your bike is on the roof, you risk damaging the roof (of whatever building you hit), the bike, rack and truck all at the same time.
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