The Pendant isn't the only way to open the sealed doors. I mean, obviously Queen Zeal, Dalton, & Magus (as the Prophet) didn't need Schala to open the door to the throne room every time they entered...I doubt many other people, like the Gurus, needed her Pendant either...
Also, even if the Dome Keeper is a decendant of Marle, I don't think that automatically connects her & Crono...I mean, it's not like he has to be a direct decendant...He could be more related to the bar keep in Porre and still be a decendant of Marle...