Yes, exactly. The guys at Walisi Yi, a camping store ON the Applachian Trail have a very negative opinion of Gore Tex in leather boots because they are hotter, less permeable and initially less form fitting than plain old leather. Walisi Yi is about 5 days in from the start of the trail and they get a ton of feedback from thousands of hikers about what is working and what is not. After having Vasque Sundowners (an otherwise excellent boot), I noticed the difference and will not have leather Gore tex boots in the future.
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Two is one, one is none. That is why I carry three.