I realize I haven't been here too long, however I've been reading the various theories, etc. in the Encyclopedia and I believe I've found one thing you didn't account for.
I believe that CC must have been based off of the ending you get before you complete all the sidequests, or at least when you destroyed the epoch. Or that the event scheme as detailed by CC must have been based in yet another alternate dimension for a few reasons.
One being that there is no way that Poore could've fielded a large enough army to defeat Guardia. If they had the elements, Crono, Marle and Lucca had magic as well. Crono alone could defeat Lavos after all, it would take a rather sizeable force to defeat him alone.
Even assuming that Poore could've fielded that large an army (and if they did have a standing army that large, Guardia must've had one at least that large as well... no country disarms when another country is still armed), if the Epoch hadn't been destroyed Crono could've fielded the help of the rest of the group (I don't believe that epoch was fueled by Lavos, and Lavos was still alive in 1005 AD anyway).
Assuming that the forest had something to do with Poore taking over, keep in mind that this forest had been regrowing for 400 years, it wasn't new and Guardia would've known about it. For them to stay in control as long as they did they must've had a capable general and some form of standing army. Once again, once a fight goes into harsh terrain, a power advantage doesn't matter (look at us fighting in Vietnam as a good example, true that we didn't have magical elemental powers, but we had napalm and bombs and bullets). As such, I find it very hard to believe that Poore could've overwhelmed Guardia, even with elements and the like, as easily as they apparently did.
Also, lets look at the timeframe. 5 years, as has been stated before, is a very short time to go from friendly and social neighbors to bitter enemies. Since Poore (in CT) had a very, very small population, it would've certainly taken them at least 2 or 3 years to gather and train a competent army, and assuming the elemental theory they would've had to been trained to use those as well. That leaves 3 or 2 years to fight a war against the largest and most dominant power in the world at that point, not to mention the people who managed to save the world from the most powerful force (by far) at that point, and it would've had to be all of them assuming the epoch still existed. I find myself extremely sceptical (spelling?) about them managing to win the war with Guardia in that short period of time. My guess? They would've deadlocked at Zenan bridge, just the same as Magus' forces 400 or some years earlier (note that Magus' troops had some magic as well, only theres was innate).
These ideas just don't add up to a victory for Poore in the required time frame, which leads to the idea that somehow there must've been a dimension change...
The deciding factor here is the Epoch, thus the split must've accorded on the decision to either destroy the epoch or not. With the Epoch, even if the war started going badly for Guardia, Crono and the group could've gone back a few years and prevented Poore from getting the elements or what not. In fact, they could've prevented this from ever happening with the epoch (with all the benefits and losses that entails). Without some qualification on whether they crash it or not, the theory just doesn't work. Why couldn't they change history yet again?
That's just my opinion though...