Your confusion is justified and I need to correct that in the program and instructions.
For the most part, Bru'n Water is geared toward producing better mashing conditions. Those mineral and acid adjustments apply to the mash.
But justifiably, you ask "what about adjustments to the sparge water". I haven't explained enough to Bru'n Water users how they should be applying those water adjustments to the sparge water.
The bottom line is that most of the mineral adjustments do need to apply to the sparge water (or be added directly to the kettle) to provide the intended ion concentrations in the starting wort. The only additions you do not want to add to the sparge water (or kettle) are alkalinity increasers (chalk, baking soda, or pickling lime) or alkalinity reducers (acids). The reasons for this follow.
Sparge water typically needs to have a slightly acidic pH to help avoid leaching tannins into the wort. Bru'n Water includes a Sparge Water Acidification calculator to help the brewer find out how much of a particular acid they should be adding to that volume of sparge water to reach that desired pH range of 5.5 to 6.0. Assuming the brewer has done this to their sparge water, they would not want to add any additional acid that the Water Adjustment sheet recommended. So for sparge water, ignore the acid addition recommended on the Water Adjustment sheet.
As mentioned above, sparge water typically needs an acid addition to produce that desired 5.5 to 6.0 pH. Since the alkalinity increasers (chalk, baking soda, and pickling lime) will typically increase water pH, it should be obvious that you don't want to add them to the sparge water. Unfortunately removing chalk and pickling lime from the sparge water additions means that you may not have the intended calcium concentration in your starting wort. There are a couple of options in this case. The first is to ignore the deficiency. This is OK unless the overall Ca concentration is going to drop under 40 to 50 ppm. This could cause fermentation and precipitation problems in the beer. Another option is to overcompensate the calcium deficiency with an addition of either calcium chloride or gypsum.