How is that? If you're referring to the fact that he appears in Home world, isn't it because he's captured in when blown off course to Another's Chronopolis and FATE made him guardian/keeper of the Dead Sea? I see what you mean when you say that Miguel couldn't have existed in the Lavos timeline, but it's feasible for Crono to exist as him in Another, since he would have existed as Crono at his age in the Lavos timeline.
Eh, I'm not entirely explaining this correctly, but I think I got the basic point across.