Think about this, the centre of mass moves backwards with your shoulders when you shorten the stem, by moving the stem upwards you relieve more pressure off the hands. By, shifting the seat forwards you move your hips and centre of mass forward so you can try to get back how the bicycle was balance previously. If you simply shorten and raise the stem the bicycle will handle differently due to the centre of mass difference. This is one reason why bicycles come with different sizes, HTA and STAs.