It is my belief that stardates work in a way similar to time zones. To wit, while those onboard a starship in one part of the galaxy might be experiencing stardate 2700, it might be stardate 3000 on another starship in a different part of the galaxy at the same moment of real time. This is so the dates can be related to one central focal point, maybe Earth or the center of the Federation.
This explains such oddities in TOS such as the "overlapping" of certain stardates, as stardate 1514.1 occurring in both "The Corbomite Manuever" and "The Man Trap". These two episodes happened very close to each other in real time, but the repition in stardates happened because the Enterprise was in a slightly different part of space in each episode. It's kind of like a person flying from the East Coast to the West Coast getting to relive the same hour twice in one day.
In the case of the odd stardate for the animated episode "The Magicks of Megas-Tu", the Enterprise in that episode was said to be investigating the center of the galaxy. This area may have been so far removed in distance from the center of Federation space that the stardate used to represent it had to be a much lower number than what it might have been had the Enterprise been closer to Earth.
This is just my explanation for certain oddities in the stardate timeline, anyway.