Ken, it appears your RO water supplier needs to change the filter. I don't know what the legal parameters are for the classification of RO water for sale or if there even are any but I can see where you aren't going to get your CO3 number down as much as you would like by diluting with it. I agree that distilled water would be a better starting point for your lighter beers.
As for the Pilsner Urquell I have no basis for a response. Some of the numbers, like Magnesium, Chloride and total hardness seem off the scale. Is Urquell adding Magnesium Chloride somewhere in the process? And if they are, why? As you said does the alcohol content of the beer skew the ion readings of the test? There is some Magnesium content in malt but AFAIK it is nowhere near that number and the chloride content is puzzling.