Just to add - Goretex allows manufacturers not only to use thinner leather, more seams, but also leather of lesser quality (you would be suprised by the difference a good leather can make, and there is only so much of really good leather available). I once had boots where the left one was significally more waterproof then the other, and the problem was definitely in leather, not the seams.
On the other hand, if you are using wax on your boots (like I do) breathability is decreased to a level where there is no difference between having and not having a membrane in your boots. So I tend to buy the boot which fits, Goretex lining not being the main thing I look for.
Justy one more thing, leather on "good and sturdy" leather+goretex boots is usually 2.2 - 2.8 mm thick, comparing to something like 4mm on traditional "one piece, one seam" leather boots.