It will depend on whether or not your two shortcuts are set up asAdvertised Shortcuts or not in the MSI package (check the Target column of the
Shortcut Tablefor the two shortcuts in question). For Advertised Shortcuts you will need to ensure that the Target column for your two shortcuts don't point to the same Feature in the Feature table and that your user option to install the 'full version' or the 'limited version' only causes one of the two Features to be installed at a time.
If the shortcuts are not Advertised Shortcuts then you need to make sure that each shortcut is associated with a different MSI component (component_ column of the Shortcut Table) and that your user option to install the 'full version' or the 'limited version' only causes one of the components to be installed at a time.