1. There is a great deal of difference between high end and low end carbon frames. Not understanding these differences doesn't make them go away; This isn't creationism...
2. Shop can't stock bikes in multiple colours because it would force shops to invest considerably more Capitol into the least profitable segment of their businesses: Complete bikes. At the end of the season they would be left with a mush mash of bikes that they would have to blow out at a loss. Not possible.
3. Factories aren't just sitting around waiting to paint your frame. Factories are FACTORIES, not your buddy's garage. It costs THOUSANDS OF DOLLARS just to run a single production line for a day. Factories only work when you scale them up so that they are producing multiple items (the more, the better) to justify the costs involved.
Customization only works at the very top end because of the costs.