Isn't everyone overreacting to the "new ending"? For one, it's the last alternative ending. Should I remember you that there's also an ending where all the planet is Reptites? granted, there is a Reptite dimension, it illustrates another possibility... and this is exactly what the alternate Prophet/Magus says.
I think the new ending doesn't follow a chronological event leading to Chrono Cross (eh, the party was wiped by the Dream Devourer, no Robo, no Lucca, no one alive), but does however illustrate an aspect of the Chrono Series through an alternate story, much like the Reptites ending does.
What I'm saying is that Chrono and the others didn't really got there to fight the Devourer, but it does illustrate that Magus did. And had his memory erased. The party being there is irrelevant. They never really faced the Devourer.