Janus is a powerful magician, and so is Schala, (who makes an appearance because of what happens in Cross) so together they were able to create another time gate to warp to Crono, Marle, and the deceased Lucca's time period.
About the Porrean rule, they aren't ruling in El Nido anymore, they are in Guardia. As you know, Porre was invading El Nido AND Guardia during Chrono Cross, and during Cross, we hear nothing about the liberation of Guardia, so it is my guess that Guardia is still under Porre control. That is why Crono and company needs Serges help.