I guess, but I don't see any difference in water that started with low alkalinity and ended up with a lot of it versus a base water with high bicarbonate.
Just the conjecture that neutralized bicarbonate (like what would happen in your acidic mash) lends an unpleasant flavor. I'm not an expert mead maker, but I've noticed it's definitely true when making mead, and also when making Belgian candi syrup. You can use much larger amounts of lime than chalk before you hit the taste threshold. How applicable that is to beer I couldn't say with certainty, but I strongly suspect similar flavor issues.
I agree, and am not a big fan of chalk either. Beers I haven't added chalk to are almost always better than the ones I have. The possible reasons are:
1) No need for additional alkalinity. This is definitely possible; AJ Delange thinks that few, if any, circumstances warrant adding alkalinity. My water has a bicarbonate content of 59 ppm. I've checked the mash pH with my meter on beers like a 60 SRM stout, and found that the contributions from a mostly roasted malt grainbill still result in a mash pH of 5.5. The same mash read at about 4.9 with the colorphast strips, which, even with the 0.3 margin of error that Kai found, do not seem to be at all reliable for dark beers.
2) Neutralizied alkalinity. Possible, but I don't see the same effect when using lactic acid in light lagers.
3) Residual chalk. Could impart flavors, given that it doesn't dissolve completely. Also possible that we are adding twice as much as we need, given the poor solubility, and the rest dissolves/reacts in the boil and causes a high wort pH. This is generally never good.
I just want people to be careful with adding alkalinity. In most cases, alkalinity is a bad thing. I'm still looking for "the answer", as well; even though generalizations about water are hard to make, there are some best practices. It seems to me that they are style based, and based on flavor. 100 ppm of bicarbonate have very little effect on the conversion, given the mash pH shift is less than 0.1, but have a large effect on flavor.