I'm going with a Rhino system as well. The one on another post attaches directly to the roof rails and the moonroof can still open. https://www.broncosportforum.com/forum/threads/rhino-rack-pioneer-installed-on-bl-bl.2734/...
From what I remember from another post that you get a front set and backset because the rail changes size. The poster said he had a like issue until he caught rail size change. Could this be your issue?