Out of all the theories presented here, I think that Marle didn't want to change the past, and thus remained in her own dimension, but everyone else used time traveling to change something about the past, present, or future, and in doing so their own dimension was split off from the original dimension, the one that would've taken place if they hadn't traveled in time... but Marle's lack of wanting to change time, rather than to change time and therefor split off into a new dimension where a new future could be possible, sent her simply back in time, not to a splintered dimension
(i haven't read anything about that 'time traveler's immunity' thing that everyone's refering to, but i think i understand the basic concept but through a different logic)
however, i don't fully believe that theory
i forget how Lucca made the gate key, and whether it was made with any special material, but i'm going to assume that it was just something that magnified the power of space distortion (the teleporter) into time distortion..
I, actually, think that Marle's pendant, not Marle's unwanting to change the past, had the ability to send her into the past of her own timeline, and thus her actions sin the past of her own timeline would affect her original 'present'.. similarly, Crono's actions in the first trip to 600 AD would also affect the present (allowing his saving the queen to fix the future and Marle), but if Lucca were the one to save her with the gate key two timelines would be created, one in which Marle did infact get sent to the DBT, and one in which Leena (was that the queen's name) was saved and resulted in Marle's continuing existance (correct me if i'm wrong, but i think that Lucca doesn't come with the gate key until after Crono save's Leena)
i forget exactly, but iirc the pendant was made using lavos' power, allowing lavos' power to bend the normal rules of time travel... i forget, since i haven't played CT in a while, when Lavos' opened a gate, but, according to my theory, the gate must've allowed the party to move through their own dimension (but, iirc, they moved into the future, so even with normal time travel they'd still remain in their own dimension)... then again, the entity's power to make gates must be higher than lavos', so i guess the entity could've had the power to make gates that go into the past but remain in the same dimension
i really want to play CT again, becuase i think the 'happy' ending of CT is an illusion, since it's just a splinter off of the timeline in which Lavos does destroy the world, which still exists, even if unknown to the people in the new-non-Lavos timeline... then again, maybe all of the gates leading into the past may have been made by the entity (disabling splinter dimensions), but in accordance with that there'd have been a lot of paradoxes, or w/e they're called, like Marle's disappearing