I think it's the most obvious thing one would think after playing the game: Lavos lives in the core of the planet, draining energy from the planet. No pocket dimension. There's one Lavos in each era. So for the events of CC to happen, I'd assume Crono and Co killed Lavos in 1000ad, so he wouldn't be alive in 1999.
That's what I always believed, since 1995. When I read about the pocket dimension thing, I thought about it as a ridiculous and fantastic idea. But that's just me I guess. Sorry ofr going "trolling" in here~
And well let's not get off-topic just because of my post. ;[