No, those are entirely different games. The list is screwy, though. Shiren the Wanderer is Mysterious Dungeon 2, but the N64 game is Shiren the Wanderer 2. Note the difference. It's like how Wario Land is Super Mario Land 3, but then Wario Land itself has a Wario Land 2 sequel.
I find it amusing looking at these lists. Americans may think the Japanese are whacked out and ask "Where's Halo?", but if a Japanese person looked at an American list, they'd be just as shocked by the lack of stuff like Tactics Ogre or Valkyrie Profile.
I can definitely relate to the tastes of the Japanese more so than Americans, but even with my undying love for RPGs, I still wouldn't make my own personal list quite so dominated by them. For one, I think the only Final Fantasy I've played that I'd put on a top 100 would be Final Fantasy Tactics.