Actually, SE stated in an earlier post (on pol), that the Chocobo raising would be implemented with 2 new colors, and eventually they would release extra colors. The two new colors are Blue and Black. Whether or not the .DATs are in the game or not, doesn't mean much, they still have time to add them in, before they're full blown adults.
As for the Breeding, its not the same as FF7. Theres an NPC in Upper Jeuno (I believe), that states that the color will be dependant on the Father chocobo. I can't remember the exact quote, but it said something like:
"If the father is blue, and the mother is yellow, the resulting offspring will be blue."
So, from the sound of it, unless you have to breed with the NPC Chocobos, Generation 1s, can be colored. However, I seriously doubt you'll see any NPC'd Chocobos, being anything other than yellow, and most likely the same with the Jeuno quest.