Chrono Trigger's general framework was laid out by another person, and I'm not sure which. Masato Kato was given the task of developing specific scenarios and events in the eras, and bringing individual happenings together. He masterminded the entire era of 12000 B.C. (now that is amazing) and took the helm of the Chrono series after Trigger. Regardless, he did not have full control over the story, and this is probably why the Marle Disappearance Paradox exists. As for the Marle Descendant Paradox, it's possible that the same clash of ideas caused an inconsistency here. It would be very easy to fix it if Marle's ancestorship were redirected to Kino, but apparently this was not addressed in Trigger's development.
It's likely that he would have fixed things were Trigger his game, simply because he wrote the entire plot of Chrono Cross. That, my friends, is scenario writing skill. It's one thing to fully comprehend the plot, and it's another entirely to have written that bad boy.