I do both. With my SBI!, site everything is jumbled in one folder. Not my ideal scenario for file management, but since it's the way SBI! does it, not much I can do.
On 2create I use the /folder/page1.html structure but it's not an extra folder because I name the folder according to the topic. (i.e. design, money, traffic, etc.)
Not really sure how to measure which one does best but I wouldn't worry about it. 2create get way more traffic using the extra folder and that doesn't line up with what the article you read says. But then again, 2create has way more content and I work on that site much more.
I think when it comes down to it, it's all about backlinks. If your site becomes popular in your niche, it's not going to matter much what structure you have. Years ago I may have answered this differently but these days I don't think it matters much.
Just as it's becoming less about meta tags, I think the other traditional SEO techniques will become less important too.
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