Not only is Gilgamesh an idiot, his whole connection to the Dimensional Rift was accidental in the first place - he was thrown into it by X-Death in FFV after all, and from then on seemed to be stuck to it (there was even an in-joke in Dissidia Duodecium where he arrived in Dissidia's dimension unintentionally, challenged whomever the player was playing, and then the Rift opens up again and pulls him back into it, Gil screaming "NOOOOO!!" all the while.).

So although ol' six arms is synomymous with the Rift, he can't control it nor determine where he ends up. It's all very vague.

And to say nothing of him being connected to the Hildibrand quest line which is not directly connected to the main scenario, as Cleretic mentioned above.