1. You're right, I hadn't actually noticed that until after I wrote the blog post. I think it's because I hide the Dock by default (still doesn't explain why I didn't notice it in the app switcher)
My point was, there are three places to manage downloads. I have to manually close the Downloads bar. Worst of all (and this is something I forgot to point out in the post) is that closing the downloads bar actually makes the browser window smaller!
2. You're right, there are nice parts of having the preferences be in the tab.
3. I didn't mean the search field covers search results, it covers the website's UI. Here's another example of it blocking the UI, this time in github: http://cl.ly/1t450T1S0s2J2V0I3O1W