I definitely would not worry about a somewhat low calcium level. Calcium is only needed for removing oxalate and speeding yeast flocculation. I've noticed that dark beers tend to clear pretty well anyhow, so speeding flocculation doesn't seem to be critical.
I've focused on only using baking soda in my last several dark beer batches and found that the flavor is improved by the sodium. Of course, its still pretty low Na content, but more than I used to use.
The flavor ions (Mg, Na, SO4, Cl) are what I tend to focus on. The Ca and HCO3 content is far less important and is likely to vary from those published profiles.