It was awhile ago so I’d have to look back on exactly what setup I was running, but practically speaking no, I wouldn’t have installed the tent with bolts that would be contacting the paint. You want a good 1/4” on anything like this to compensate for body/frame flexing when off-road, maybe less of an issue on the roof, but a good general rule.
Every manufacturer likely uses different sized hardware, specific to each tent and general application. The brackets themselves may also be proprietary. That said, the actual nuts and bolts should be standardized in metric or sae, meaning you can swap the included hardware out for shorter/longer bits as needed.
Installing aftermarket crossbars isn’t a bad idea, but it will raise the overall positioning of the tent above the roof. I like to keep things as low as possible, so the trade off of a few extra minutes to install the tent was more valuable to me than raising it another inch or two above the roof. It also saves $$.
Importantly, I also knew an aftermarket rack was in my future. If it wasn’t, the Thule/Yakima crossbar option may represent a better value.
I’ve since gone to a Front Runner, then back to a Gobi Stealth like I had on my last 5th gen. Overall it’s the best system for me, but there are other confounders at play aside from the tent.
For a stock rack, it makes the most sense (to me) to save the money spent on aftermarket crossbars and install the tent directly to the rails. A few bucks on shorter bolts is money well spent. If you’re installing and uninstalling the tent frequently then perhaps the crossbars make sense. That’s your call. Hope that helps!