When I piece, anything goes! I often use serger thread to piece in fact, since someone gave me a lifetime supply and I don't own a serger. I don't care at all if the top and bottom match.
When I FMQ, I almost always match the bobbin to the top thread. It really hides the little mistakes I always make (usually moving the fabric too fast....). Even Leah Day suggests using matching threads when FMQ.