I think it's mentioned elsewhere, but the Proto Dome gate likely led to Medina Village in 1000 AD. If you compare the maps of the timelines from each end of a gate, they match up very close geographically. The Proto Dome is perhaps the best match of all, as it sits practically directly ontop of the house in Medina. It's odd though that the 2 gates arent opposite each other in the end of time. But why is the 65,000,000 BC gate there?
Well, I think that its opposite must be the bucket that leads to 1999 AD. If you think about it, these 2 eras are perhaps the most significant in the the history of the planet. The date Lavos arrives, and the date he rises.
But as to why the 1999 AD gate is seperated from the others, perhaps its something much more simple. Gaspar comments that people have been dropping into the End of Time recently. Perhaps he moved the 1999 AD gate over closer to himself, so he could warn time travellers to avoid that gate. And he does just that, he warns Crono's group about the 1999 AD gate the first time you talk to him. I assume he has the power to do this, however it seems logical. All 3 gurus performed some fantastic feats, Gaspar's being the time egg. Since the End of Time really has no fixed point in space, perhaps moving the physical entrance of the gates is childs play for someone such as him. Or perhaps Spekkio did it? Either way, its still moved.
Though this would be much more clear if the 65,000,000 BC pillar of light and the 2300 AD one simply changed places.