Yes! Cargo box was selected specifically for its lower profile so I can also run my WeBoost Reach antenna a few inches higher than the cargo box and still clear the garage. Top of cargo box with 35's is 92.5" garage door is 96" to the rubber weather seal and another 3/4" before I start contacting the door frame. Plan to adjust the WeBoost antenna so it just touches the weather seal. This puts most of the functional element of the antenna above the cargo box giving a 360 degree view of the horizon. I'll have it on a folding marine mount so I can jump out and flip it down if I need that extra few inches to clear a parking garage. Do you do the same with yours, or just remove it entirely when not out in the sticks?
FYI - I followed a slightly modified version of your fit guide prior to installing the tires. Went and flexed it out last night and could not produce any rub. Fully flexed, full lock in reverse, in low mode, etc. No touching anywhere and tons of clearance on UCA with the 1" skinner rubber. Body mount is about 5/8" clearance at it's closest point so I may go ahead and chop it just for peace of mind.
I remove my trucker antenna when not out in the sticks. Actually, now that I have a directional yagi antenna on my camper, I find myself using the trucker antenna less. May sell it. I think your antenna might be okay in relation to the cargo box because composites shouldn't appreciably effect radio waves.
Sounds awesome that the 35x11.5s practically drop in. That size may be the ticket and really wouldn't give up much, while having some incremental advantages in efficiency and weight.
With as big as these tires are, I find at high inflation pressures (high sidewall spring rate) with higher freeway speeds and mixed with really broken pavement, that the damper settings in comfort may not provide enough damping for good wheel control. Sport setting can solve it and make for a more controlled and comfortable ride in these situations. Great to be able to adjust on the fly.