Yes, the whole thing is rather confusing. Baby Kid is clearly wearing Schala's Dreamstone pendant in the PS/DS ending cutscene of Chrono Trigger, but she doesn't wear it in Chrono Cross as one would expect of such a sentimental item. I suspect the pendant in the cutscene was simply intended to be visual shorthand to help establish Kid's origin and bridge the two games; in "reality" she was wearing the Astral Amulet. Or an even simpler explanation: it was the result of an oversight on the game developers' parts, or a miscommunication between them and the animation studio.
As for Kid holding her beaded necklace in the Chrono Cross ending cutscene, I think that was probably just meant to identify her to the audience; there's no mistaking such a distinctive item.
Although you raise an interesting point about the possibility of the pendant changing shape. Dreamstone items have been shown to be quite malleable. Just look at the many evolutions of the Ruby Knife: from knife to good Masamune, to evil Masamune, and finally to Mastermune. However, I seriously doubt Kid's beaded necklace was intended to be the Dreamstone pendant because no fuss is ever made about it in-game.
Both the concept art and the in-game sprite of the Dreamstone which Ayla gives to Crono depict a large chunk of red rock rather than a blue necklace. In any event, the circumstances surrounding Leah are so strange that I think it's impossible to draw any definite conclusions about her.