Not sure exactly what you’re seeing but the 3.0 has a valve that looks kind of like the valve on gas trucks with cylinder deactivation to reduce drone and improve exhaust sound when using varying cylinders. On the diesel however it’s a bit more complicated.
It helps with engine braking when in Tow/Haul mode, the valve closes to restrict exhaust flow, which increases backpressure to assist the transmission in slowing the truck down
Also, it helps the motor reach operating temperatures more quickly and I’m sure has emission implications (like DPF regens, etc) - I suspect removing it could throw codes. Might do some google work.
And it may not even be your sound at al? but I would start at the dealer to see if they can isolate the sound before deleting the flap valve personally. There are at least a couple guys on here that work on these and have way more hands on knowledge and might be able to chime in (and correct anything I might be off base on)