" The theme registry has been rebuilt. Turn off this feature on production websites. "
I think this warning is too obtrusive for something which is displayed constantly. The warning area shows all warnings from Drupal, not just this one. It's risky to display it constantly like this - the user just starts to ignore everything in it.
I also find it's more difficult to tweak the site layout with these warnings always near the top of the page. It breaks the WYSIWYG aspect of site design.
I suggest adding a new option on the theme config page that allows the user to switch the registry rebuild warning off.
Obviously these warnings are important. So here's a two ideas how they could be made less obtrusive, but still effective:
1) Allow the user to switch off the warning, but only for a limited time (like two hours), or...
2) If warnings are switched off, then force the display of the warning only when the number of users connected rises above a low threshold, like 5. So if the site goes live, the warning should appear.