Yep, I'm aware they're not normal shortcuts, that's why I specified "Advertised" shortcuts.
And as I mentioned in my post there is no issue with the normally created shortcuts. However, there are drawbacks. For instance the Advertised shortcuts keep a history of recently opened files associated with whichever program. And without the registry modifications I mentioned above if you tried to open a doc/xls directly it would results in the same Windows Installer prompt as opening one of the Advertised shortcuts.
Most likely a repair or reinstall would fix the issue, but in the situations where that's not possible I'd like to have a fix rather than an workaround. If you (or anyone else) can think of something else to try towards that end it would be appreciated.