Marle's pendant may have come from a parallel dimension.
This way, Marle's is a different pendant from kid's one, which was originally Schala's one. Two pendants, two dimensions. That's a theory.
almost correct the pendants looking different was just a design change, or its ment to look like that when not in the gold holding thing.
marles pendant came from the original timelines schala (passed down,found, or however the royal family got it) before crono and co started changing it, kids pendant is the one schala had in the changed timeline where crono and co's presence changed what happened to schala so she kept her pendant in that timeline which then got sent to kid.
parrallel dimensions are different from timelines in a few ways.
If there is only one pendent, How did all those other people get through the doors? 
I'm guessing that Alot of the Enlightened ones had pendents of some sort that could open their boxes and doors. I'm guessing that Marle's pendent is just one of the remaining stones that wasn't kept in the treasury, but passed down,and that Schala sent hers to kid.
think of those as treasure rooms / high security doors. you arnt just gonna hand out the keys to them. besides schala was there to open shit like that during the time when the enlightened ones ever needed to open them for whatecer reason.
as for the pendent appearing in marles royal familly theres probably some crazy law that prevents paradoxes like that by allowing the item to exist even if its existance in the past is altered so it appears elsewhere from its original appearence.
otherwise we would have cause multiple paradoxes and the chrono universe would be forced to cease to exist. or something like that
