Let me lead off by saying that water treatment is a personal choice.
That said, the author's rules are not backed with good data. The author suggests looking for cold water, while other authors point out that giardia cysts survive longer in cold water, making it more risky. The author suggests using fast moving water, some have suggested lakes are safer as giardia cysts tend to sink in calm water. The author suggests avoiding main streams, other authors say main streams are safer because "dilution is the solution." The point is, these are theories without solid data to back them up.
It is human nature to believe in our own experience. In threads like this there are usually people who've gotten giardia after drinking backcountry water. I'm one of them. Will someone's experience match mine, or someone who has never gotten sick? There's no way of knowing.
The EPA says Cysts have been found all months of the year in surface waters from the Arctic to the tropics in even the most pristine of surface waters. Another quote from that paper Hibler (1988) found Giardia cysts in 19% of springs. Look at that paper and do a search for "pristine" and see how often giardia is found in even pristine waters.
Some people can build some immunity over time to various waterborne diseases, but there are many strains of giardia. I've had giardia three times and it's easy to find tales from other hikers who have been stricken multiple times over many years, just as it's easy to find hikers who rarely or never treat and have never gotten sick.
The incubation period of giardia is usually 3-25 days, but can be as little as 1 day. The Dr's reported onset was on the 4th day after drinking the suspect water.
Sheep DO sometimes carry a strain of giardia that can infect humans, as can many other species of animals.
"Giardia and crypto are also easily shaken off by a healthy adult." Sometimes. Sometimes not. Several backpackers appear weekly at Centinela Mammoth Hospital in Mammoth Lakes sick enough with giardiasis to need urgent care
"Incidentally, there is no reason to get too worried about cow manure near the water." ...animal manure can carry many pathogens ranging from Giardia to Salmonella to E. coli. Here's a fact I recently uncovered: Giardia-infected cattle excrete nearly 100 million Giardia cysts per day Dr Robert Derlet.
Unfortunately while researching this I was saddened to learn that the author of this article, along with his daughter, lost their lives in the Colorado mountains in 2011.