I'm no scientist, but one thing does come to mind....
mineral composition of the brewing water.
As you increase the water temperature, you increase the rate of evaporation. When water evaporates, it does so in the form of pure water vapor.
Therefore, as the water evaporates, the concentration of minerals w/in your brewing water increases (because the water is evaporating, but not the minerals).
The longer water has been standing and/or left at a boil, the higher the concentration of minerals/TDS in your brewing water.
If your hot water tower is in frequent use (i.e. getting fresh water constantly) fluctuating mineral content should be a negligible issue (although I would measure it to be sure!). However, leaving water at a boil without any way of adding in fresh water, would be the worst case -- as it will continue to increase in mineral content (as a %).
Along those lines, I also don't recommend serving the water that is dispensed from a steam boiler on an espresso machine, as it is prone to having a higher mineral content than the brewing water.
I think the recommendation to "bring to a boil, then rest" comes from the notion that, without a thermometer, this is a better/easier way to arrive at the correct brewing temperature.