A few minutes of Googling is not enough.
San Francisco has been treating Hetch Hetchy water with Chlorine or Chloramine since long before Rockwell wrote his paper. In 2004 they switched from chlorine to chloramine.
In a controlled environment, like a modern treatment plant, over 99.9% of giardia cysts can be killed using chlorine or chloramine, (source: Optimizing Chloramine Treatment, Gregory Kirkmeyer, Kathy Martel) which is the safety level the Surface Water Treatment Rule standard requires, so your point about treatment effectiveness is invalid.
I DID talk personally to the water treatment officials and they told me the cyst level count was at the intake. But even if the testing IS done on the output, 99.9% plus (and 99.99%+ of viruses) of those cysts would be dead after treatment so Rockwell's point is invalid regardless.
It's silly to compare city water which is tested on an ongoing basis with a real-world water source which has likely never been tested in history and if it has, likely decades ago.
You quoted Derlet above. From a 2010 article Where do you get infections in the wilderness? The most obvious possibility, he believed, was the water.
Now, after 10 years of fieldwork and 4,500 miles of backpacking, Derlet knows for sure. What he has learned, after analyzing hundreds of samples dipped from backcountry lakes and streams, is that parts of the high Sierra are not nearly as pristine as they look.
Read more here: http://www.modbee.com/2010/05/08/1158938/fouled-waters-sierra-lakes-streams.html#storylink=cpy