I was curious how/why Growl was doing things this way, so I did a little 
digging. The following article is extremely helpful:
http://www.delitestudio.com/2011/10/25/start-dockless-apps-at-login-with-app-sandbox-enabled/

In a nutshell:

   - Sandboxed (i.e., any App Store apps) apps can't access the file that 
   controls Login Items.
   - Instead, they provide a helper application that lives in the main app 
   bundle in *Contents/Library/LoginItems *(this approach documented 
here<http://developer.apple.com/library/mac/#documentation/MacOSX/Conceptual/BPSystemStartup/Chapters/CreatingLoginItems.html>
   .)
   - The *SMLoginItemSetEnabled* function can be used to register the 
   helper app with launchd so that it runs on user login. The helper app 
   launches the main app before terminating.
   - Apps that use this approach do not show up in Login Items.

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