We have had a tonneau on both our most recent trucks. We love them in there as it keeps everything out when not being used.
On our 2012 ram it was great we had 5.5 inches between the tonneau rails and the front cap.
Never had an issue.
On our 2016 3500 it sat so much higher that when we lower on the new trailer we had about two. We thought we could get it home with no issues. Did great till our driveway. We tinked the driver side rail. Ever so slightly.
Once the hitch was installed it raised it up enough so now we are just shy of 5.5 inches.
But we love having it on there.