I see your point about #3, but to be honest, I've been using Chrome since v1 and I have never once had this be an issue. Not a single time. There is simply never a case where what I'm searching for is in the very top right 10 pixels of a page. In your github example, why would you ever be searching for "dashboard", "inbox", "account settings", or "log out"?

Also I don't really understand your complaint about the bookmarks bar. Why do you have it up at all if you don't like the UI? If I want to go to a bookmarked page, I hit ctrl-shift-b to bring up the bar or, much more often, I open a new tab. I think the thing that separates Chrome from other browsers is the huge content real estate, and keeping the bookmarks bar up there takes away from this in a big way.