It comes from when he became a SAG member. Matt/hew Miller is a very common name, and when you become a union member, you need to have a distinct name. All variations of "Matt/hew Miller" were taken, so he chose "Mercer" (a family name) as his stage surname. (This is info from various panels he's done at conventions.)

He is pretty hot and so is his voice. I wonder the same thing about the surname.