Absolutely. The purpose of "Pre-shading" is to get darkened panels, which will then be minimized by more paint. Do not eliminate the dark areas, simply tone them down. "Pre" denotes the dark painting before the final color.
Think of it as a blending step. It will tone the contrast between the colors down. What you want is a subtle effect, not such a stark one. You are kind of giving the paint some depth, adding that third dimension...
Hope this helps.
Scott