Dunno about under exposing but I agree that straight out of the camera the RAW's look slightly flat, dunno about JPEG's as I never shoot them.
If it's JPEG's that you're talking about I think it'll just be down to the 5D being an older design. Like my 300D, 10D and 20D the output will look flat when compared to a newer camera as these days the output is a lot more punchy, back in the day the output was a bit flatter as it was assumed that people would want to process their own shots.
I never bothered with the in camera JPEG tweaks, but I assume they'd help to produce a punchy JPEG straight from the camera.