That I know of no one in the US has a MySky yet. There may be some in Canada and Overseas in Europe that have a version. So it may be a while before someone can truly give you a accurate answer.
But this is one thing I also wondered myself for a while but figured it won't be a problem. If you look at the
Mopar video of the MySky at time-index 0:05 thru 0:10) the My Sky panel does rise up to the level of the side rails and then slides back. Most crossbars rise above the side rails and it should be okay and not in the way for the MySky to open.
As for removing the panels, I assume the crossrails have to placed at two of the yellow lines I indicated below.
and attached at either A & B or B & C
I don't think placing the crossrails at point A and C is durable since that's quite far from each other. But so long as the first crossrail is at the mid way point of the two panels and the second crossrail is behind the real panel they won't be in the way of removing the panels.
Now mind you I don't even have a Renegade and I'm just going by the videos and photos so my analysis may not mean much. Hopefully MySkys will start coming in and we'll get an answer from someone willing to test my theory.
Oh and btw Welcome to the forum.
TS