In general, I agree with the premise of the article: specifically, Priceline and Hotwire typically yield the lowest cash cost, but not necessarily the best value.
For flights, Priceline has never been an option for me because I don't take Priceline-candidate trips (e.g., flights where I truly have zero opinion about when I fly, what airline I use, and what route is used to get me to the destination). Therefore, I've never even reached the question "Is it worth giving up FF miles/perks to save X dollars?"
For rental cars, I've simply found that Priceline usually can't beat the best combinations of corporate/promotion codes at one or more agency sites for most normal rentals. (Priceline's niche, IME, is specialty cars and the specific rental lengths that aren't well-supported by the agency sites, such as 5 days, 9 days, etc.)
That leaves hotels. I think we all agree that this is where Priceline has the big potential to save us some serious cash in exchange for giving up hotel points and perks. But just like a well-informed bidder can get the perfect Priceline win, saving 50+% off of the points-earning rate, a well-informed user of the other travel sites (both booking sites and research sites like FT!) can frequently find deals that are competitive with Priceline in terms of overall value.
For example, I have an upcoming stay in an area where 3* hotels cost $44 (give or take a couple bucks) + $6 fee on Priceline. There's my opaque baseline: fifty bucks for a perfectly acceptable Courtyard or Sheraton.
Then I go to Expedia and Travelocity and find their advance-purchase rates for similar hotels for $69 for a similar hotel. $19 more to lose the "opaqueness", but similar no-cancel and no-points rules. Priceline is still better.
Then I drop by FT and notice new thread about 5000 AA miles with a Sheraton stay. Hmmm. Then I browse the Marriott board and see which Promotional Codes are allowable for general public use (e.g., M11, M12, etc.).
Finally, I find an $84 room at the Sheraton that would quality for the 5000 miles and I find a $74 1-bedroom suite at a Residence Inn on a "Holiday Promotion" rate that includes free breakfast, evening cocktails, a 6PM day of arrival cancel policy, and Marriott Rewards points.
In this case, Priceline is clearly a distant #3, or perhaps #2 if we assume that the Average Joe doesn't value 5000 AA miles like we FT'ers do.
The point is: you have to investigate all avenues for all stays if you are truly concerned about best overall value. If Consumer WebWatch didn't do this skillfully for all sites involved, their statistics don't really mean much - even though their overall premise has merit.