I assume you mean the full width flap (rock guard) right at the rear bumper?
I canít see how it would. Both the engine and genny exhaust are well forward of where it would mount (at least on our 2016). We bought ours in September, and it had an aftermarket rock guard already in place.
It also had standard factory installed mud flaps behind the rear wheels.
2016 Tiffin Allegro Open Road 32SA
2017 Jeep Wrangler JKU