The DS version of CT actually suggests that Magus might be Guile post memory wipe. In Trigger, Magus claims that if a piece of himself should remain, maybe his new self would be able to save Schala, as he realizes that he would never be able to save her as he was. Upon waking up, he has no clue where he is nor who he was...but he feels he must find "something" and that he will search to the ends of the earth to find it.
Fast forward to Guile in Cross, and we learn that Guile is in search of the world's enigma. He has no clear motive, just that he is looking for abnormalities. This lines up with what Magus says at the end of Trigger when you fight the Dream Devourer. He even states when you talk to him as an NPC after recuiting him "take me to the enigma", as if finding "something" is his only real motivation. Given that he was originally planned to be Magus, the resemblance is already there. The differences in personality can easily be contributed to Magus wiping his memory, and therefore not knowing of his past hardships that made him who he was before. With that in mind, it is widely believed that Magus was retconned to be Guile omce again with the DS content, but in a way that does not compromise Cross's story.
But for the sake of conversation, lets pretend that the DS ending did not happen for this discussion. In this case he was already planned to be Guile (but with his memory) similar to how he was Magil in RD. He would likely join during the Viper Manor break in, as a nod to RD as well. Saving Kid would no longer be an option, at least one where he would remain in the party. It is possible he could leave temporarily if you choose not to save her and find a way himself.
Post body swap, Magus would likely rejoin before you got your body back after crossing paths and fighting with him out of confusion (similar to Radius). Kid is alone with Lynx now, so he would want to shut that shit down real fast.
Aside from that however, he really would just be another vessel for translating the plot of Chrono Cross. Since Kid is not Schala herself, he would likely have been tasked by Balthasar to watch over her, and Magus would already know everything that is going on. He would just be going through the motions until the time was right to reveal himself, similar to how when he was a false prophet of Zeal.