While in this case it is simple user preference, in other cases it could mean an accessibility concern, or even give room to malicious attacks: With all these custom browser skins, pop-ups over the HTML body (link destination on hover) and no clear divide between window and application, users won't clearly know the difference between interaction with the browser, and interaction with a smart malicious website.
With smart design one could make the bottom browser toolbar appear to be higher, and control the top half with your website. Fake plug-in install modal windows etc.