The machine does not know the status of the aircraft. The procedure for calculating Vapp for failure cases is purely manual based on QRH tables.
The VLS is real time speed and is always correct for the present configuration. When there is slat or flap failure the Vapp is not known that time. That is where QRH given addition gives you the target Vapp but when you select Conf3 to land the VLS even with one surface jammed is correctly calculated and you land at that VLS.