As you close the skin, the pivot point is at the trailing edge. If the stiffeners are going to be close to the spar, if not trimmed, the outside edge could contact and scratch the spar while closing.
Although probably not an issue in this case, tapering a stiffener is also sometimes required to spread the stresses along the length of the piece. If it is not tapered stress concentrates at the end of the stiffener whereas if tapered, the stiffener gets less and less stiff along the taper and so absorbs any stress along its length.