Gil may have been Magus in Radical Dreamers, but I honestly don't think they are the same person in Chrono Cross. Here are a few reasons why.

First, Guile has absolutely no recollection of certain events, characters and places that he should have if he's actually Magus in disguise. If you beat the game with Guile in your party, he doesn't even acknowledge Schala. All he does is say something like "well, it's been good traveling with you Serge. See ya!" He also doesn't react at all if he's in your party when Kid reads Lucca's letter. At the end, the letter basically says that someone in your party is Janus, which was Magus' name as a child.

Second, their personalities are nothing alike. Guile consitently proves himself to be a compassionate, level-headed person throughout CC. Magus was a cold, distant and dangerously pragmatic tyrant. Magus wouldn't go out of his way to act in a fashion that was the exact opposite of his nature unless it served some advantageous purpose. In the case of Chrono Cross, pretending to be someone else wouldn't actually benefit him in any way.

Third, why in the hell would he be in disguise? Magus isn't mentioned once in Chrono Cross, so it's safe to assume that nobody either knows who he was, or cares who he was. So, it would also be reasonable to assume that he could just walk around as Magus and not have to worry about any problems arising. It would have gone against his character for Magus to wear a disguise and act like a completely different person unless it was beneficial to him, like the Prophet disguise he used in Zeal.

Finally, If Guile is Magus in disguise, how in the name of living crap did he manage to relocate himself from the year 600 A.D. to 1020 A.D. without the use of a time altering device and without any time portals left to use? After Lavos was destroyed, all of the portals closed up, as is seen in the game's ending! Now, I say "600 A.D." because that would be the most likely place that he would be sent. Either there or 12,000 B.C. Either way, he didn't stay in 1000 A.D, and there was no available way for him to travel through time in order to make it to 1020 A.D. just so he could dress up like a birthday party magician with a wand and a mask!

Here's my theory. Guile is an alternate reality version of Magus. Throughout all of Chrono Cross, we see many characters featured in both Home World and Another World, and in many cases, they have differing personalities. So, it's not unreasonable to assume that Magus and Guile are respectively the dark and light sides of the same coin. Here's a really poorly drawn example of what I'm talking about.

----------Magus--------------------------Guile
-------------------\---------------------/
---------------------\-----------------/
-----------------------\-------------/
-------------------------\---------/
---------------------------\-----/
-----------------------------\-/
------------------------------|
------------------------------|
------------------------------|
------------------------------|
---------------------------Janus


My theory is that, sometime before Janus became Magus, his life split down two separate paths. One path took him to becoming Magus, and the other made him Guile. My assumption would be that when Janus was drawn through the Lavos Portal at the Ocean Palace (or whatever the hell it was called) that is where the division took place. The darkside Janus was dumped out into the year 600 A.D to be raised by Ozzie and become a dark warlord, and the lightside Janus was dumped out somewhwere around 1000 A.D. on the Zenan mainland.

One way or another, I don't see how Magus and Janus could be the same person. Plus, I think it would be really friggin' lame if they were.