Just to clear something up... bicarbonate is part of the ionic report, alkalinity is a measure made up of carbonate and bicarbonate ionic content. A lab report will provide carbonate, bicarbonate and total alkalinity as CaCO3 (usually) or as mEq/L. When these are stacked in the spreadsheet and the math is attempting to compute the ionic content and then factor both the water's Alkalinity and Residual Alkalinity, the result can be a negative ion number when compared to a given target water profile. BWS at least shows those differences. In the latest version, RA and Alkalinity are removed from the Water Adjustment tab, however Bicarbonate remains at the top as an ion... attempting to show the differences between the target profile, your existing water, dilution water and the final water result. >>> Hence confusion. BWS asks for Total Alkalinity as CaCO3, not as bicarbonate as inferred. I have found the spreadsheet to be a very useful and accurate tool as I have been exploring water chemistry. I also found AJ's proton deficit spreadsheet useful and educational, but without the proper reporting from maltsters or the time to run test mashes on every malt I use, BWS's model is working for me. Brewer's Friend or EZWater can likely provide good results once you have used them enough to understand their particular behavior.
In my opinon, when matching a water profile (should you choose to do so) priorities should be Sulfate, Chloride and Calcium. You may choose to also match Sodium and Magnesium or ignore them. After you have matched your ionic targets, you need to adjust your Estimated Mash pH (after your grist and mash/sparge water volumes are entered) to your desired level. In most cases, you will simply need Lactic or Phosphoric acid to drop to your preferred estimated mash pH. If you are using 100% RO, you may need to raise your mash pH with an alkali (or reduce your use of calcium bearing mineral salts) when using a particularly "hard" water profile like that Pale Ale profile, which will affect your ionic concentrations and require some tweaking to the salt additions. Never use both acid and an alkali in the same mash.
As for how or what profile or any treatment, that is a personal choice. As you can see by looking at the many recommendations throughout this forum - everyone has different ideas of levels of sulfate or chloride or even what mash pH to target. I have lots of opinions - none of them are anything but that. As you brew with minerals, you need to experiment with how you want to approach this and tweak the process to your preference - including if relying on spreadsheets, programs and meters bring anything meaningful. I happen to believe that this attention to detail has improved my brewing practices.
I happen to like some sulfate in my hoppy beers and some chloride in my malty beers, but a mix of both is even better - but would never have discovered that without brewing and practice. I have also discovered that I like a little magnesium and sodium as well. All that said - there is no scientific basis here - just my pre-biased opinion of what worked and didn't work in a given recipe. Always take anyone's opinion with some skepticism and determine what you like best.
I suspect I brew a few lagers and British ales that AJ would really enjoy as they closely follow his recommendations, and a few American Pales that he would politely decline to finish.
Someday I hope to find out! It will take me many years to become as experienced or educated.