Page loads on pre-4.0.0 instances where theme_stacking has not been set throw a warning:

Notice (8): Undefined index: theme_stacking [APP/Controller/AppController.php, line 955]

Instead of using CoSetting->find, AppController should use a function added to CoSetting, such as CoSetting::themeStackingEnabled($coId), that uses CoSetting::lookupValue to perform the check. A similar call could be used to obtain the co_theme_id.