I read that article in the morebeer link back when I was working on a recipe. That hopping schedule, pitching/fermentation temp, and two hour boil are each part of my process. I also long two step Hochkurz type rests at 143 and 158 and mash out. I have done it both with and without decoction and, ultimately don't notice a huge difference in the end product.
As for water treatment, it's your beer, do with it as you please. That article says "they must adjust the water during the mash," but does not say with what be it acid or salts. I always adjust the mash with acid, but as for adjusting the water profile from RO, I have done it with minimal added mineral content to mimic the Pilsen water as well as adding CaCl2 or Gypsum to the boil. In my case, surprisingly, a gypsum addition resulted in a beer that was the closest by my palate, but all were very good. But the only way to really know is to try a variety of approaches and judge for yourself.
With this style, the biggest contributor to that distinct Czech pils flavor is time. The flavor from the saaz hops changes pretty drastically at about the 6--8 week point.