Lets see it this way.
We need to tie in genetics.
Ayla has blonde hair. Ayla looks almost like Marle. Kino is a direct ancestor of Marle. Kino + Ayla made offspring that one day made the Guardia Royal family and that family had decendants that included Marle. And from Marle (who looks like Ayla. You know Kino look like Crono XD) goes on to have the Director of Arris Dome and Doan.
For the Zealian royal family, and if you take away all that hair dying bullshit (which it is), the Zealian royal family is most likely related to the Lubarians (forgot the spelling). They seemed smarter than the Iokan's anyway, which might mean they were the ones who found the flame first, and it explains why Zeal was like one of the first enlightened ones because she harnessed Lavos' Magic etc.
As for the pendant, there are many explanations to that. We do not know exactally, but I do not believe that it is a true Guardia heirloom. I would have rather thought that theres a possiblity that Queen Azalia found it somewhere and gave it to Marle, and that is why she holds it so dear to her.
Because her pendant is uncharged, it is most likely that Schala died in the ocean palace (or was reincarnated by the original timelines flame and did exist somewhere in 1000AD, and possibly was the child that Lucca found in 1004AD [before the timecrashed timeline]). So hence the pendant gets passed around anyway, or is found.
Basically, Queen Zeal only had Schala and Magus. Magus never had kids because he died in the original timeline, and as for the new timeline after 1020AD - i'm all for Lucca and Magus lol (unless Serge is the reincarnation Oo).
And Schala most likely never had kids, except in RD. In RD, her reincarnated self and Serge met up. The child who is reading Serge's journal is the grandson of Serge and Kid.
And because Schala and Magus never did have kids in their own timelines, Marle being related to them is unfounded.