From recent interviews - FFTA2 actually does take place in the real Ivalice - that's one of the reasons they decided to put Vaan, Penelo, and Al-Cid in as playable characters. In fact, translated character and story details put the setting somewhere in the Rozarrian Empire after FFXII and RW. The devs even stated that FFTA2 is set after FFXII and that we'd see some familiar faces from FFXII.

Also, keep in mind that Matsuno wasn't the sole creator of Ivalice. Many of the staff that helped him create it is still working on the Ivalice Alliance. Finally, just because Matsuno left the company doesn't mean he won't ever work with them again.

Also, I'm not looking for historical answers or major revalations, just how the map fits together as a whole in the context of the 5 main games(again not counting FFTA).