I have read into this - basically .... a padded saddle can be more uncomfortable. Essentially when you sit on it, some of the padding is displaced, some of this paddingis pushed upwards - this presses against something on you bum that it shouldn't press against. Similar to the reason why you shouldn't place weight on the palm of your hand in between the two "balls" (On the palm of you hand, just above the wrist there are two lumpy/fleshier parts... one being right at the "bottom" of the thumb. Between these lumps, pressure shouldn't be applied or the world comes to an end.
Padding on shorts is positioned so that it does not press up, hurting the bit which is not to be hurt.
Sorry - I have no scientific knowledge/terminology, but this is the reason why we like padded shorts and unpadded saddles.