I know I am coming into this topic rather late, but I would like to add that as an RPG Chrono Trigger uses abstractions such as the lack of cities on a continent or the size of a sprite in relation to the size of a house maptile.
Therefore the presence of Latin, AD, and BC could simply be an abstraction representing the "nearest equivalent" in relation to their world.
The development team, rather than devise new terms and language, likely used which ones they felt would quickly and easily represent their intended meaning. So a literal analysis may not be necessarily possible. Generally history is divided up by each new epoch. The Victorian Era began with the coronation of the Queen Victoria. The Inter-War Period began with the end of World War I.
In Chrono Trigger the timelines seem to be focused on the transition from one epoch to another. For instance in Prehistory you see the fall of Lavos and the end of the Reptites. This could easily signify the end of the epoch into a new one. In Antiquity you see the fall of Zeal...again the transition from one epoch to another.
AD 600, the end of the War of the Mystics...again the end of an epoch.
AD 1000 is within an epoch, but apparently does not end until Porre destroys it. This may or may not be the end of the epoch, thought if AD is an abstract term literally referencing Guardia, then it likely would be. However, as AD 1999 and AD 2300 are recorded as they are, it could mean that the calender system in reference to the founding of Guardia was not dismissed. At least by Gaspar.
AD 1999 is the end of recorded history. A new epoch, the last epoch, begins.
AD 2300 is a time within the last epoch, where there is no possibility for history to continue.
It is likely, however, that the robots under mother brain, providing they one-day achieve global domination, would put in place their own calender, which may or may not even have significant relevance to the Gregorian one as robots would see little purpose in emulating a human system.
Now, I cannot recall if anyone in the game script uses the term AD or if it is just for when using the Epoch. Regardless, I believe that if you want to explain it via plot it likely would be a method of recording history from the viewpoint of Gaspar using the 1000th year of Guardia as a starting reference point.
That is my two-cents.
