Shorts and underwear are different items of clothing worn by a player. Undershorts are underwear, not shorts. 4.4f prevents padded shorts from being worn, so cannot apply to undershorts. Padded undershorts are not specifically prohibited, but neither are they specifically allowed to be padded either (Regulation 12). If you would not allow padded socks, nor sternum or rib padding protection (Regulation 12 only permits shoulder padding) then you can require padded shorts to be removed (but separate rib padding would be allowed as a corset). Equally, depending on level, you could permit these items as long as the padding is not thicker than the general prohibition of 0.5cm when uncompressed (Regulation 12). The player could wear the padding that is in his undershorts as a (presumably crotchless! (no thank you Dickie)) support under Law 4.1a.
I've got bigger things to worry about than players' padded undershorts. Nor would I worry if he/she was wearing cycling shorts as underwear - they would not be required to remove the saddle padding.