Doing some rust prevention on a '16 Ram 1500. I see they still put the foam between the box side and the outer wheel well support. This has got to be a big sponge and probably contributes to the rust problem these trucks have.

Has anyone tried removing it? How did it go, and what did you do to rust-proof there?

I do not have a newer truck with the foam in the wheel wells ,but I under coated my 2001 Dakota from down south with a clean body. The first thing I did was drill holes on the inside of the bed sides above the wheel wells, two holes on each side about a half inch in diameter so an undercoating plug will fit, I sprayed in Rust killer neutralizer ,then let it sit for 24 hours, next step I took some Eastwood frame spray with the 24in hose and nozzle and I ran it up one side and across and then up the other side and across the inner wheel wells between the outer and inner bed walls and let it fill in all the nooks and crannies and cover as much surface as possible

You might try acetone in a spray bottle, but that is some nasty stuff. Gloves, goggles, glasses, and fresh air needed. As always, try a small area first.