Variable Phase Order implies that turns may not be played the same way as before and / or after.
With Puerto Rico, every turn is different, depending on who starts selecting the roles, and what roles they take. You may have to play the 'build' action sooner than you'd wish depending on an other players move, or with other games, you may be denied from taking certain action.
Most games with limited action and any game without a static turn order fall under this 'mechanism'