I am thinking that Martin and AJ should chime in on this question as the experts... but here are my two cents.
I think in terms of priority - as such:
1.) Get the mash pH right. Good extraction seems to contribute the best flavors.
2.) Determine what flavor expression you wish for your beer. This can be from research, a style recommendation or personal preference. Bru'n Water profiles are an excellent starting point.
3.) Personally, I focus on ions in this order: sulfate, chloride, calcium - then on magnesium and sodium. Most (in my experience) styles work fine with just sulfate and chloride adjustments, with calcium naturally falling where it may. Other people may have a completely different approach and opinions.
4.) Look again at the predicted mash pH and - if needed - use an alkaline or acid addition to return to a good mash pH.
Martin has pointed out that many excellent beers, especially pale lagers are brewed with very little calcium. There are many benefits to having reasonable calcium levels in the mash (as an enzyme co-factor, protein precipitation, lowering mash pH), but low calcium should not prevent a great beer. My beers have improved a lot by supplementing calcium through gypsum and calcium chloride, but my saisons and wits are brewed with less than 30 ppm calcium typically. I have been pushing up the gypsum a bit lately in my saisons to get a rougher bitterness. A careful focus on pitching very healthy yeast, proper oxygenation and proper fermentation seem far more important than an arbitrary minimum calcium requirement.
Magnesium and sodium are slowly creeping back into my beers at low levels, but I remain cautious in recommending, because a little can go a long way. They are strong flavors to me. I brought in a bit of magnesium (25 ppm) into my last pale ale but cannot tell if it helped the beer or not yet. My opinions should not preclude experimenting with magnesium. You should note that the Primer avoids table salt and Epsom salts.
I think to the heart of the matter, you would only divert from a given style profile (or other recommendations like in Bru'n Water or the Primer) for preferential reasons. If you like a given profile - there is no reason to change from it except to experiment or refine. It seems that personal preferences of sulfates, in particular, can vary widely. If for example, your APA tastes minerally from a high level of sulfate and chloride - then you should dial back the additions.
Hope this helps!