When you have the site offline and are logged in to the manager the site acts normal so you can work on the site. This is actually a feature of MODx. Try logging out of MODx and viewing the site. You should see your site unavailable message.
That is one beautiful, sweet little feature. It means you don’t "have to" move from staged to live--you can develop live. Sweet. Nice. Time-saving. Did I say sweet?