I only had one unpleasant flush in terms of balance and that was during a flush in which I had drunk oolong tea during my only meal of that day. The next day my electrolytes dropped and I became quite dizzy. Fortunately, I had an electrolyte beverage handy and found almost instant relief after a few swallows.
Like you suggest, I have found that the more balanced my calcium and magnesium levels are before my flush, the more restful and relaxed I feel the day after. I don't develop the overall dryness that I did when I was low on alkaline minerals.
I can't speak to the Science of it all, but I can say that experience certainly validates the concept.