Why exactly do you assume that the WC3 colour is the "original" colour? If anything, WC1 would be the original colour.
And, all things considered, it's more than a coincidence. We encounter WC2 ships primarily in Enigma Sector. Presumably, they're not manufactured by one of the nearby clans. The WC3 ships are probably manufactured on Kilrah, since their colour matches the WC3 manual description of Kilrah-manufactured plasteel. Similarly, Priv ships, manufactured somewhere near Gemini have a completely different shade.
Another explanation could be the alloy used for the armour. Apparently, the WC3 Kilrathi ships use plasteel. We know, on the other hand, that WC1/2 Kilrathi ships used durasteel.