It is not the spring that rubs against the intake, but the spring seat adjusters. They are a larger diameter than the spring. So the larger spring diameter isn't a problem.

I got the stock spring rate (5.6) off the Race Tech website. The 6.2 I installed is stiffer.

 

Yes it can be the length of the new spring, when the sag is set properly the adjuster and whatever washer or seat you use can be in a place where it can rub. It can seem like it clears but after a few rides you can see it. .49 , 6.4 F R, I'm 190.