Tiles missing after Start Menu repair (following MO497128)

So I'm sure you are all aware of the issues caused by the bad Windows Defender definitions tail end of last week, and MS has put forward a PS script in order to help put Start Menu shortcuts back (GitHub - microsoft/MDE-PowerBI-Templates: A respository for MDATP PowerBI Templates). I have found in my testing for my organisation that while it does put back the shortcuts, our Tiles (which are controlled via an Intune Configuration Profile) are still broken. It is as if the DesktopApplicationID specified in the XML no longer has any meaning. Anyone else run into this at all, and if so any useful info as to what might help?