Some use mortar as a filler, you can lay plastic over the mortar, and that way the two materials do not touch.
Most of the time, if you set the deck perfectly, and then drop the tub, it's not perfect. To leave a one inch gap between the bottom of the tub, and the floor allows some ridges or piles of mortar that will flatten out to the right level when something is dropped over them.
If mortar is applies in a full coat, then it's the same as guessing with wood. You want the little bit you put in to be able to squish out and find it's right height.