When hiring staff for Tokyo RPG Factory applicants were not told that the studio was part of Square Enix. Yosuke Matsuda (CEO of Square Enix) wanted to hire people who were passionate about RPG's, rather than people who wanted to work for Square Enix.
Square Enix founded Tokyo RPG Factory to develop this game.
I Am Setsuna has huge references to Chrono Trigger and Chrono Cross.