The proper way to do this according to the guy that did my bumper and by a few guys on The Corral is to use flexible bumper repair compound (epoxy). My bumper was sanded with a very coarse grit and roughed up in the area where the letters were. Then he filled the area with the bumper compound and then a layer of thin mesh was used that helps reinforce the epoxy once it dries sort of like using rebar in concrete. It was all sanded smooth and has held up very well. You can't tell that the letters were ever there.
He also told me that if you use regular body filler, the change in temperatures could actually cause the letters to "shrink" enough that they would pull away from the edges of the letters and either crack or fall all the way out if the paint cracked deep enough.
I did it because I liked the smooth look of the '03 Cobra bumper and the black relief around the exhaust outlets. It gives me a unique look with OEM fit/finish. Also, I was never impressed with the styrofoam-filled louvers/vents in the GT bumper.