Short answer is yes. The tonneau does use up some space and if you aren't careful you can hit it with the trailer. It takes a fairly tight turn combined with a dip or hump. I never did hit mine and only came close once.
But, when we changed trucks I chose to not have a tonneau cover. Got a tool box instead. The kind that is flush with the rails of the truck.
2017 Eagle HT 29.5BHOK (sold)
2017 Ford Powerstroke 6.7, Crew, 4x4 (sold)
2018 Toyota Highlander
Maggie, Old English Sheepdog