Variable Phase Order implies that turns may not be played the same way as before and / or after.
Using Puerto Rico as an example, 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. In other games, you may be denied from taking certain action.
Most games with limited action and any game without a static game turn order fall under this 'mechanism'. Use of variable player turn order are not Variable Phase Order games.