So I figured out what is going on. It's all got to do with some subtle issues on this line:
Key="SOFTWARE\$(var.Manufacturer)\!(bind.property.ProductCode)\DesktopShortcuts">
As noted in the question the documentation and references suggest that the Path for files and registry entries are used to dynamically generate the Guid. Note the path includes the file/Value Name. This is in fact happening but how was I getting the same Guid for the ComponentId for 2 different installers using 2 different ProductCodes? You would think that the inclusion of the ProductCode into the path would make each unique. Well, turns out it's because I was using !(bind.property.ProductCode) in the path. Binder variables don't get substituted until the Linking phase with light. The Guid="*" element is generated in the Compiling phase with Candle which is obviously before the linker. So while the substitution was occurring and the proper keys were being generated in the registry, the Guid was being generated from a non unique path:
SOFTWARE\MyCompany, Inc\!(bind.property.ProductCode)\DesktopShortcuts\Installed
So don't use binder variables in any KeyPath element when using the auto generated Guid functionality.