Originally, I also thought the DSD would be revealed as the mother dragon. However, after thinking more about it, I'm thinking the DSD isn't the mother, but still WITH the mother in the Unending Ocean. There's plenty of room to hide something down there, especially if it's asleep or somewhat inactive. It could be that the Mother is actually The All and birthed the Dragons to balance out Tyria's magic. She could be Tyria's analogue to Gaia in what she represents and her role in creating other high level beings (in this case, Dragons). In these Mythologies, there's usually at least one "kid" that's loyal to the parent god, so that may be why the DSD seems to stay out of the chaos the others engage in.