There are alternate antenna stay mounting holes to use when you have the trunk guard rails. The antenna moves out just a smidge which is enough to clear the rails. Just look at the top of the chrome square bar that the OEM antenna stay is mounted on. There are three holes. The outer two are used when you don't have the guard rails. The inner two holes are used when you do.
Exactly right. You just need to move your antenna out. Use the outer holes, and it clears the rails.
MP