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When we override a URL like chrome://bookmarks by an extension, it maps it to
the chrome-extension:// url, but should still display the chrome://bookmarks
url in the omnibox.  crrev.com/5fafa5aa changed
the way prefs were read, so it broke this.  Fix the breakage, and add a unittest
so that it doesn't happen again.

BUG=579389

Review URL: https://codereview.chromium.org/1635663002

Cr-Commit-Position: refs/heads/master@{#371824}