Since no two people are ever going to paint two models exactly the same, I don't think its that big of an issue. I mean, I've seen fleets of EA that looked like someone had a grabbag of skittles when they picked their colors.
As long as it gives the painter a good idea of the style of how ships look, techniques in how to get certain effects (vorlon skin, or drazi engines, etc) then slight variances in color are a non-issue