The water volumes entered into those categories should be the actual amounts used.
For some brewers, the 'actual amounts used' might vary. Some brewers prepare a large volume of water that is more than they will actually use. In order to get the ionic concentrations correct, that full volume needs to be entered so that you dose the salts properly.
However in the case of the mash, the mashing water volume MUST be equal to the ACTUAL amount of water that you'll be adding to the mash tun. It doesn't matter if there unrecoverable deadspace or volume in the tun, all volume must be included since that extra water does influence the chemistry of the mash. The mineral salt dosing for the mash must match that actual mash tun volume.