Mine is F250, with Retrax rolling cover.
But I think they are all going to clear a cover. Unless you had your hitch head adjusted up above the level of the bed sides, and I don't think any normal setup is going to do that.
However, the release handle may hit the cover. Many of us have shortened or otherwise modified the release handle so that it doesn't stick up. This is something I would recommend on a Reese hitch whether you run a cover or not, because in my opinion that release handle sticks upward far too much.
Also, when I am not towing and the cover is closed, I use a bungee cord to keep the hitch head tilted toward the driver side. That keeps it from banging around while I'm driving, and also keeps it from tilting so that the release handle would hit the underside of the cover.
It all works together great actually. When hitched up, the rolling cover goes right up next to the pin box, locks there, and keeps weather off the front end of my bed and also reduces air turbulence toward the rear of the bed.
2006 F250 Diesel
2011 Keystone Cougar 278RKSWE Fiver