There is one reason I can think of. Now is it a "good" enough reason? I don't know. And this is based on what I know of the JK top. I haven't been able to tell yet if it's the same or similar on the JL.Doesn't really look like there is a good reason why the 3-piece hard top can't have removable side windows.
But on the JK, the sides are where the bolts are to secure the top onto the tub. If they were removed then there would be no connection there to the vehicle. Now dies the JL have another location on the rear curve to place a bolt? Don't know. If not and it's similar to the JK, there's a reason.
However, as I understand it currently, the theory is the hard framework of the sliding top is not removeable. So it must be attached in that rear curve location. How it's done can be the difference in the 3-piece allowing for removeable sides.