First off: Let it be known that the Compendium's purpose is to find as close to absolute truth as possible, but it is not necessarily for the sake of merely "knowing" the truth. Rather, it is something much more akin to what your theory serves for you, GoA: Many of us--myself and Zeality included--are doing this so that we might write fanfics that are as close to the true spirit of the Chrono games (and can therefore be read as complements to the games); finding theories that the majority of Chrono fans, or at least Compendium users, can agree upon helps us toward this. So in other words, we won't be promoting your theory because it's far from what we would want to use, not because we think it's just absolutely wrong. You're right, we can't prove it wrong, but you can't prove it right either.
That said, I would very much like to see you expand upon it in a fanfic. It might even be one that I read, as it sounds interesting. You see, "rewritings" of the game, or telling it with a somewhat different or highly interpreted--the latter of which yours would be--plot aren't usually up my alley; I prefer to read fics which take place after the game and try to tell a new story in the feel of the original, or stories which either fill in holes--like what happened to Guardia, what happened to Lucca after she was kidnapped, etc.--or expand upon individual scenarios, maybe adding a little--like the FFVI fanfic I've been wanting to write for a long, long time expanding on the whole Crescent Island scenario in the World of Balance--to be among my favorite types of fanfics. Sometimes I also like crossovers or fics that retell stories from a different perspective than the game follows (like my two fics that are posted--in their beginning stages--at
http://www.icybrian.com/fanfic/ybrikmetaknight ), but only if they're done well. In other words, I'm not sure I would read your fic just based on my personal taste in fanfics (although I might, because it intrigues me), but I certainly think many others would like to read it. Hell, it's been a long time since I've really read any fanfics; I'm somewhat ashamed of myself in that regard. *hangs head in shame*
With regards to my statement that you need to think outside the box, I believe you interpreted it slightly differently than I meant. I meant that you've been taking things very literally, specifically that the presence of A.D./B.C., a European-styled kingdom, and religious institutions or symbols like churches and nuns to mean that Christianity literally exists. And so on and so forth with some of the other things, like Latin, Greek, etc., which is why I used Final Fantasy games to make a point, and why I brought the Masamune into discussion (it still blows my mind that CT/CC's Masamune is clearly a broadsword whereas the Masamunes in other games, along with the real-life namesakes, are katanas). I meant that your theory took a lot of things very, very literally (it's now obvious to me that that's on purpose), and that's what I meant when I said you need to think more outside the box. A little miscommunication on my part there.
You should type out longer posts in notepad, or at least copy and paste them into notepad before you submit. Helps save yourself from frustratingly having to retype them.
And I would like to debate the scientific validity of evolution in another thread, perhaps in general discussion, if you wish; I'll let you make the first comments and start the thread. I would just personally like to see your thoughts on the matter.
Finally, I think your theory is viable (if for no reason other than that we cannot truly, absolutely disprove it), although farfetched.