Actually, I have an answer, but it's going to take some thought to present correctly. It is anything short of simple, given the adverse nature of time travel in any given story line.
First of all, think of the End of Time not as an extension of the CT-World, but outside of it. It has it's own time-keeping mechanism there, which is not the same as in the CT-World, yet it is. I will explain in due course.
Now, in the Storyline wherein Lavos destroys the world in 1999 AD, Belthazar is shipped off to the distant future, 2300 AD, where he eventually dies of old age/sickness. This proves that the Guru's are Mortal and prone to the same limitations as all mortals. So how come Belthazar dies and Gaspar and Melchior do not? Let's say... situation and chance. The other two's situations are inherently different from the cold, bleak surroundings that Belthazar was put into, for one. And, to have this question about Gaspar, it must be about Melchior, too, even if they are in different places and times.
Only so much time passed between their exile from the Kingdom of Zeal and their interactions with Crono & Crew.
If you notice during the normal gameplay, no matter what you do in one time zone, time still progresses forward at the same rate in the other time zones. When you spend a day in 600 AD, a day is spent in 1000 AD, as well. You are thinking of the End of Time as being one lone stretch of existence from the beginning of the time to the end, but it isn't. It is a time zone as well. Just one that connects to all others at once. Now, given the rules stated previously, when Gaspar and the other Gurus were exiled from Zeal, they were all sent their separate ways along with Janus. Each person spent the same amount of time in each time zone. That is the key. Gaspar didnt spend any more time than the others just because he was at the End of Time.
Gaspar is still aging the same as the others, at the same pace.
Now, how the End of Time got created... that would make for interesting conversation. I'm guessing it was created when the three gurus and Janus were exiled. No more than 3 people can enter a time warp at once, but you bet Gaspar didn't learn that until after his exile. When the four of them traveled through space and time, the gate couldn't handle the stress and so a new place and time was created out of nothingness. Seeing as how all points of time came to being after the beginning of time, and since it encompassed all era's of time, it was probably best decided by Gaspar to be labeled as the End of Time.
