Don't study man. Drop out. Drop out and play Chrono all day. You know you want to.
Fair enough. There is no evidence suggesting that Lavos "exits" his pocket dimension because that would hinge on the pocket dimension existing in the first place. So that portion of my argument is unnecessary.
The fact that Magus remembers them in 12,000 BC is a huge nail in the coffin for the PD theory. I can't believe we didn't think of that before. It makes me wonder what other insanely obvious things we haven't thought of.
So we can infer a few things from this fact -
1) Eclipse Magus had to come from a dimension in which he met Crono and co. and was sent to Zeal, thus initiating the New Ocean Palace disaster.
2) The events surrounding the fall of Zeal probably proceeded very similarly to how things happened in the dimension that the main game story takes place in.
3) The fact that Eclipse Magus mentions that they "may or may not have teamed up with him in their dimension" suggests that he
did team up with Crono and co. in his. Otherwise why would he mention this? Plus, he would have been killed by them in the fight.
So, this evidence strongly suggests to me that Eclipse Magus is probably
both from another dimension
and from the future of that dimension.