In a nutshell: The App Store indicates that apps need to be updated even when the apps are current on the Mac's internal drive. The App Store "sees" the apps on a cloned external drive and wants to update them. In some cases the apps are current and in one instance the App Store wants to update an up-to-date app but the button is grayed-out and reads "installed." 
After communicating with Apple they let me know that they consider Time Machine to be the "approved" backup mechanism, so they don't consider this to be a priority to be fixed in a future update.
Folks who are interested in all the details can check out the SuperDuper! forum thread: http://www.shirt-pocket.com/forums/showthread.php?t=6733.
After communicating with Apple they let me know that they consider Time Machine to be the "approved" backup mechanism, so they don't consider this to be a priority to be fixed in a future update.
Folks who are interested in all the details can check out the SuperDuper! forum thread: http://www.shirt-pocket.com/forums/showthread.php?t=6733.