I don't think there's a definitive answer as to why the originals had in the white cylinders. I've seen it said that it had to do with the iron or that it's because Colt didn't want to weaken the cylinder further by heating it to blue it. But I don't know what the actual reason is.
And you're correct, Colt made 1000 for the military contract, and an additional 100 for commercial sale. So there were 1100 made in total.