Welcome to the forum. Looking at the pics of those steps, they do appear to stick under the flare a pretty good ways. Hard to say if there would be interference or not. But the Mopar flaps hang down on the inside of the fender closest to the tire. So it may clear. But, like said, hard to be certain.
FWIW, if you are looking for any kind of protection out of those rails, I would urge you to look elsewhere. Those are steps and nothing more. I would encourage you to look into something like the ACE rails
which do a good job of providing a useful step as well as protection when offroad (and from those pesky door-openers next to you in parking lots). The ACE rails looks great, especially when mounted in conjunction with Rubi sliders.