If you're using a low calcium water that produces an acceptable mash pH without adjustment, then an enhancement that the wort will need is a dose of calcium to improve yeast performance. Since adding calcium to the mash has the tendency to reduce mash pH, that calcium dose can be added directly to the kettle instead of the mash.
Yes, the calcium dose can be calculated using the kettle volume and the intended calcium concentration would be produced in the wort. The question is what should that calcium (or any other ion) concentration be in the post-mash wort? The mash has the tendency to add and subtract ions in comparison to the initial water concentrations. Given that ambiguity, I recommend that a 'close enough' philosophy be used. Just ignore the ionic gains or losses in the mash and add your desired ionic concentrations directly to the mash.
I too disagree with Gordon's lack of accuracy that results from adding dry minerals volumetrically instead of by weight, but the simplicity of his water adjustments would not penalize him too much. And I can't argue with his results. Plus, I understand he does use a pH meter to check his mash pH. And as mentioned above, the ability to consistently reproduce a given outcome and assess minor changes will come to those who brew a similar beer time after time and dial in all components of a beer. Gordon rebrews and tweaks with great effectiveness.
Unfortunately, that is not how most brewers brew. I do enjoy brewing certain beers over and over. I do tweak with each sucessive batch, but I also want a tool that is going to help me get in the ballpark the first time and subsequent brews. Gordon properly coaches for brewers to not mess with their water too much. Since he typically brews with RO water and the RO process is 'messing with your water to the max', what he really should be telling brewers is, 'don't add too much mineral content to your brewing water'. Brewing with RO or distilled water is a luxury that some brewers don't have access to. Using a program like Bru'n Water is an important step in understanding what your water is and what the effect of adding minerals will be. Unless a brewer is using RO water like Gordon does, the water adjustments he uses could be disasterous to your brewing.
With all that said, I too use RO water for my brewing since my tap water is not suitable for brewing. As RichardT suggests, if you're using RO or distilled water, you can skip Sheets 1 and 2 in Bru'n Water. You just dial up the dilution percentage to 100% and figure out your desired mineral additions. And since distilled water and RO water have very low alkalinity, it is not necessary to acidify your sparge water. Sparge water pH is NOT the real criteria we need to concern ourselves with, its reducing the water alkalinity to low concentration that is the real concern.
As RichardT finds with his Weizenbock, brewing with RO water has its limitations as the grist color increases. A source of alkalinity is needed to keep the mash pH from dropping too low. I put that red pH signal to relay the findings that I've experienced. The mash pH is very non-linear as the pH drops into the very low 5 range. The mash has to have a really high net acidity to drop the pH that low. Its my experience that a beer mashed at that pH is overly tart and rough. Even a 5.2 is really too low for my taste.
I agree that the Munich profile is a bit much for many of the lighter styles that have been produced in Munich, but it is well suited to the dark styles. To brew those lighter styles, the boiled Munich profile is much more appropriate.
All great questions! And yes, pickling lime is quite powerful. Don't even think of using it unless you have a good scale and also tend to underdose it instead of overdose.