I'd like to add something to you theory/comparison between Bekkler and Zeal. I just noticed earlier, that if you beat his copy game (the one where you follow a clone of your character) after saving Crono, you get to keep the clone you played against. Basically, if you beat it with Ayla, instead of Bekkler saying "The clone will be at Crono's house" and putting the clone of Crono in his room, he says "The clone will be at Ayla's house" and he puts a clone of Ayla in her hut (which is in the prehistoric ages) .
He can do that with all of your characters too.
How does he go through time and put the clone there, he has no gate key to go through the gates, and even if he did, the only gate in 12000BC is on an abandoned island (Magus' clone appears on the North Cape). How does he even know where they live?
The thing is, when you go to fight Zeal in the Black Omen, the room you fight her in has clones of each of your characters, odd isn't it?