Dude, Zaper, it looks like you didn't read his post. If Lucca's first theory about Marle was right, then the game's story would've crashed IMMEDIATELY as soon as Marle went back in time. Unless you wanna call that a plothole, too. Sentenal's right, just because Lucca figured out exactly what calculations and whatnot that got the already-present gate to open at will didn't make her understand exactly what she was doing or what she was working with. In fact, she wasn't even positive until she walked into the castle and realized for sure. Then she made a theory, that was proven false by every event in the game, based on Sentenal's explanation.
Sentenal didn't say there were more than one group of Crono and co. He said that if Lucca's original theory was right, then there never would've been a video documenting Lavos' destruction of the world, so Crono and co never would've seen it, and a big-ass paradox exists. Obviously things can be changed in a way Lucca didn't quite grasp in her initial understanding of time travel and time changing, right? This seems to heavily support the TTI theory, as far as I understand it.
To be honest, I'm not sure what Sentenal's point about the sealed chests was...would you mind elaborating on that, please?
Then your explanation of what happened with Marle was...well, it showed a lack of comprehension of the overall effect of time. In 1000 AD, everything in 600 AD has already happened. All of it. Right? Or it wouldn't be 400 years later. That would've all already happened, making it supposedly impossible. If Leene had indeed been killed in 600 AD, what understandable explanation is she would've returned to a time where she had never been born, much like how Serge went into a dimension where at that same point in time as the dimension he had come from, he had been dead 10 years. See what I'm saying?
The bit about Marle being returned bit by bit isn't totally insane, but it seems to fit more with your idea of relationship development between characters applied properly by the Entity, not simply because it 'takes time to reassemble the body returning from the DBT'. If Serge and party retreat from the battle with TD, you don't see them being reattached each time they leave and return, do you?
About Lucca: Lucca was brilliant, we all know that. But she wasn't always as knowledgeable and experienced as she is by CC. She was constantly learning all the time. She was just as human as everyone else was.