I ditto what
@4x4junkie said, maybe make it removable. I love all the lights and stuff above, but it does hurt mileage and performance at speed.
I didn’t see anything about bed loading. If you put a big load in the bed of the truck, won’t that make the bed and hence the cap and the rack rock round more?
Two other thoughts. If you ever have it loaded where you think it will be close, how about using some of that foam pipe insulation around the lowest bar of the front of the cap. I use that stuff for everything. You’d have to cut it around any perpendicular supports or webbing, but you can hold it on with a half a dozen zip ties or even some tape and just throw it away after. And even with that foam, if you think it might contact the top of the cab when you’re running around in the mud and dust, you may want to just run a few layers of masking tape on top of the cab where the foam would rub, just for the week or weekend.
My 87 four-wheel-drive, and my 96 F250 have rain gutters over the doors. I have a cap and roof rack on the F250, but when I carry a really long ladder or a 20 foot piece of iron or such, I have one of the very old fashioned temporary roof racks/bars that locks into the rain gutter like mom and dad had back in the day. I think they are from mom and dad actually. I have one set up for the F250, with a spacer on top, so if I put a long ladder or such on it, it holds it up higher than the cap rack, so it doesn’t hit my code 3 lights by accident. The cab wiggles different than the bed, but I’m never doing it long enough to damage the ladder or the racks. Even if your truck does not have rain gutters, they make universal racks with suction cups and straps to hold it on.
Like the temporary foam above, maybe rig your temp rack/bar underneath your basket, so it would never hit the roof of the truck. Or, you could put it across your roof in front of your basket, and run a couple of extensions on the basket, so it hits the rack instead of the top of the cab, or maybe even zip tie the extensions to the temporary bar. This also helps with the load rating of the roof of the cap. I guess my point is to create a wear spot and support spot with a bar, instead of figuring out your roof is the wear spot by accident! & Those extensions could be temporary, like a piece of conduit or even PVC pipe, held on with some zip ties or such for the weekend.
My 2cents, hope it helps!