So long as we're tossing around crackpot theories, I'll add another to the mix (though going back and answering the original question).
"Before" the events of CT (whatever that means), it's assumed Marle went and married some guy who wasn't Crono. This was a sensible, intelligent man, who was able to avoid war with Porre. Guardia's line continued to hold strong until 1999, when it held the Arris dome and the Administrator was a decendant of Marle. The bloodline continued to 2300 with Doan.
Then Crono started murking around with things. Through going to Zeal, and battling Lavos first hand, he became corrupted by the power of Lavos. (The game establishes in a hand-wavy sort of fashion that this phenomina does in fact occur to humans.) Crono kills Lavos, saves the future. However, Marle falls in love with Crono and marries him. Now, there's something about Crono that makes him not handle Porre as well. Maybe he's too used to violence? Maybe it's the taint of Lavos? Maybe it's the fact that he refuses to talk? Whatever, point is, Crono "causes" Guardia to fall.
Now, the Arris Dome doesn't even exist in the future timeline. Instead of Arris, we get Chronopolis. (This makes Doan's appearance at the Twilight Parade even more paradoxical, but meh, we'll ignore that.) The events of CC happen after all of this, so it fits.
