The 2006 hardtop has no side vents. The 2006 vents are in the tailgate. The vents are an air release that makes closing the last door open, easier to close. Without the vent, you will be compressing air inside the Jeep, making the door hard to close. (It is hard to close even with the vent). You may have to close the door, then lean against it to get the door to latch all the way in.
But you can still use this top. And if the problem is too great, you can look around for an '03 to '06 vented tailgate.