When I picked mine up it was the middle of winter and I didn't have a garage. I asked my dealership to remove the soft top for me and they wanted to charge me for an hours labor...
I played the warranty card and they seemed confused. I explained that if they did not remove the soft top I would be forced to drive home with it like that and again they seemed confused, like it was a non-issue. I then pointed out that they sticker on the soft top said driving the vehicle with both tops installed may cause damage and something to the effect of void warranty.
I told them I'd take it but I'd be leaving the soft top like it was until the summer and if there was damage they could replace it then. At that point they relented.
Seemed like a battle for something petty but it's stupid for it to be shipped with it installed like that.