Custom setting e3 does not matter if the SB-600 in in the hot shoe. E-3 only effects the operation of the built-in flash.
The Nikon support rep must have misunderstood you or had his "cheat sheet" open to the wrong page. I recommend that you always ask questions here on Nikonians before trying Nikon support. You are more likely to the best possible answers from members here with a lot of hands on experience. This Nikon support reps cannot possibly have firsthand experience with every camera that they field questions about.