The few references that Vagrant Story has to Ivalice are ones connecting the game to FFTactics (which takes place 1000 years after FFXII) and are obviously meant to place the game as the last in the Ivalice timeline since some of the things are a holy relic belonging to Agrius and a reference to Historical King Hyral's (Delita) grave.

Though I do remember the Tactics team saying after they finished War of the Lions, they wanted to return Vagrant Story. They've worked on Tactics Ogre remake since then but it may still be possible Vagrant Story may be in our future as an updated port like WotL.