I scale all grains by % to account for efficiency differences in a recipe, or when brewing a bigger, 'imperial' version of something I already brew - up to a point. If I'm trying to brew my version of a commercial beer or hit a particular SRM on a style, I want to hit the SRM pretty closely, so I'll vary the specialty malts as needed to hit the SRM I want if software puts me off by much. No reason to be overly rigid.