It isn't really clear what happens to everyone after the fight with the Dream Devourer, do they all get sent back to their own timelines/dimensions? If so, Cross probably takes place in the
What the prophet seeks timeline...allowing the player to decide on their own what canonically happened during the normal Trigger new game (most importantly Magus dying or not) without really affecting what happens in Cross, as Eclipse Magus is probably needed to become Guile in the "Prophet timeline".
Also, it's interesting to note how in TE Schala sends the party away like she originally did during the Ocean Palace incident, while she sends Magus away through a portal, like young Janus and the guru's not much later after the party during said incident by Lavos' presence (in the normal timeline anyway).
The portal might be there because Kato wants to explain this Magus will not return to the same time/timeline as the rest does.
Dalton's victory over Guardia is also indeed easily explained this way: if Dalton, who may be from either or both timelines, goes to the Prophet timeline where none of the heroes are aware of his plan...hell, they might even be dead already.
The way Schala talks to her little brother in this ending might be because she knows him better than he does: she probably knows what the result of that conversation will be, which, thinking like an older sibling, would indeed be the right thing to do...allowing him to have peace of mind instead of infinite regret over something he cannot change. She obviously still thinks of him as little Janus, not the battle hardened warrior he is now.
Also, there still is no way two Magusses are able to appear in the same place, because like Zeality said, no one in the party is able to encounter an older him/herself... but an alternate one is quite possible.
* If Future Magus really were from an alternate dimension, why would he be searching for THIS dimension's Schala? And this would also mean that the Darkness Beyond Time is connected to infinite dimensions (one DBT per infinity), which creates all sorts of probabilistic issues with the creation of a Time Devourer, which is capable of destroying the universe. Basically, as long as the probability of a Time Devourer forming is greater than 0 (and it is, apparently), then all existence would have been destroyed by now.
He probably doesn't know it's an alternate dimension...but that matters not, what matters is that the Dream Devourer is made up from the Lavos' and Schala's from at least two of those infinite dimensions. Also, apparently any creature in this dimension is incapable of affecting anyone or from before it's creation, so Lavos from 1999 can't just return to an earlier point in time.
