No, it has nothing to do with the type of URLs or whether you use mod_rewrite. I have a basic 3.8 site using the out-of-the-box URLs and my site looks like the site in the first image on google (site name and six areas linked under it). This is something google itself controls. I think it has to do with the amount of traffic going to your site and the most popular forums or areas on your site.
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