Normally I would walk-away from any dealer asking for a non-refundable deposit. But in the case of Individual Paint, I can understand as there is some risk to the dealer (should you back out of the deal).
Not many people want to pay the 5k premium for paint. I have seen this waived if there is buying history with the same dealer.
In-terms of guaranteeing the build with your preferred color, I have read this before and it is in BMW's court.
What color are you considering?