I think it has to do with the exact tension needed for what you are asking. If you use different colors on the top and bottom, any tiny bit "off" on the tension and it will show. When FMQ, that is hard.
When you are talking contrasting everything (fabric on both sides and thread on both sides) you are asking for a "pain". That may be why you haven't seen it. Leah Day suggests using the same color thread for top and bottom to more or less hide the problems that might come up if you don't use the same color. By using the same color, the problems are hidden.