Clutterfunky

Not exactly- Agate is on the opposite side of Reborn's map compared to Orre's. It does mean that the two Regions border each other, though, and that the border shifted at some point between Pokemon XD and Pokemon Reborn to make it so that Agate swapped Regions on said map. 

Now look back through Reborn and note how often Orre is directly mentioned in the game (the train in the Chrysolia Forrest is a particularly notable one, IIRC). Even the truth regarding Agate City was foreshadowed this whole time~

I've never played gale of darkness so I didn't know anything about it so I probably missed a ton of references and dont remember any of them, you'd have to quote them , I can't remember anything about a train, is that still there even if ive beaten everything up to the current story's end?

Yeah, the train never leaves (much to its former conductor's dismay)- it's technically supposed to serve as your hint regarding how to find eevee, as well as slip a cactus pokemon into your hands well before you have access to the desert. It's pretty dang neat in general, if I do say so myself!