I see tons of folks posting that they run 35x12.50x20 on leveling kits, 4" lifts, and 6" lifts with no running and no need to cut any plastic or modify/remove the crash bars.

I went and drove a friends 2015 4x4 with 6" RC lift with said tire size and her truck rubbed in some places and will definitely rub when off-roading on uneven surface and turning. No idea on wheel offset. They bought the truck this way.

Is there a difference in wheel well size between years or models? Or more possibly due to poor choice of wheel offset by whoever built it?

 

15 and up are all the same except for the 17 and up Raptor which has bigger fender bulges.

 

A very important variable that you didn't mention is wheel backspacing.

The factory wheel rims come with a pretty aggressive tuck into the wheel well. Most aftermarket wheels that people fit have a backspacing that positions the wheel further outboard, which has the effect of creating more odds of interference with parts of the suspension or body when steering.

Crash bars are another variable, but they generally don't factor in until you get above 33in diameter, 12.5in widths, or significant backspace reductions.

 

I've wondered if you can put a larger tire on the stock wheels vs an aftermarket with more back spacing.

Some owners are running some pretty good size tires on the stock wheels.