When eggs are first lain they are a bit pliant. I don't know if that lets the color penetrate better or not. Sometimes colored eggs will vary in color shade. Maybe the glands are more up in the chicken than the site I was reading mentioned. I know a lot of my maran eggs would have scratches on them that where white cause it scratched off the color... I noticed my OE eggs look like they have a very, very light blue tint on the insides for about 6 or 7 seconds then it turns white. I found that interesting. I know if you are trying to figure out who in a flock of pullets is laying you can put food coloring in the vent the night before and it will be on the egg when they lay.I thought the color added was only on certain breeds, ie. BCM for one. Their eggs are dark but you can wash the color off where as say a Welsummer's eggs are dark but its in the shell not a coating.
ETA: some of my EEs have eggs with colored shells all the way through, some not. So I guess my confusion is: If its added how does it penatrate some breeds' eggs and not others?