Since I never read Stereophile in the "good old days" when presumably they were better than they are today, I take their reviews for what they are - a chance to list the positives of the gear they review and way to spin the negatives. And of course, measure the equipment. I love the measurements, not as a way to review the equipment, but sometimes as a way to know what to look for when I get a chance to audition or listen to the equipment listed in the magazine, or even when I'm reading reviews of the same equipment elsewhere, without the accompanying measurements.
I still think Stereophile does mention things about equipment that I immediately take to be negative, except they probably don't sound totally negative when they're said, more like they're just characterizing the equipment. But if you read carefully they are listing negatives about the equipment, usually immediately followed by platitudes or "lets put this in perspective, I'm only saying this is a shortcoming when compared to equipment 5x more expensive...." That and you will see a tell tale lack of enthusiasm about some equipment they review, which to me is a kiss of death.
The negative comments in the measurements are almost always straightforward, sometimes including remarks like "I'm surprised that the reviewer found this equipment so transparent in the high end, when I see these problems in the measurement."
I do agree however that readers almost need a guide to interpreting Stereophile reviews. In the last 5 years I have read several reviews in stereophile that made me decide against buying equipment, and a few reviews that sparked my interest enough to make me research equipment further.
I think the real fallacy is to think you can make up your mind about any equipment purely by reading reviews about equipment, whether that review is in Stereophile or a forum.