It isn't any more mixing than Square's already done with Kingdom Hearts, really. Chrono Trigger is officially recognized by Squaresoft as part of the Final Fantasy genre; while not actually bearing the FF name, the game was originally intended to be a Final Fantasy title (as evidenced by Square packaging it in with FFIV for Final Fantasy Chronicles). So yes, Magus and Ansem are from different games, but KH does incorporate popular FF characters alongside the Disney and KH-only ones, making characters from the Chrono series fair game for cameo or even plot-important roles.