@EnterpriseArchitect,Thanks for posting in Q&A.
From your description, I know that you want to patch third-party applications or update them via Intune.
Based on my research, you can deploy third-party software package, it is suggested to use win32 app via Intune.
https://video2.skills-academy.com/en-us/mem/intune/apps/apps-win32-add
And we can add Win32 app supersedence to update this app.
https://video2.skills-academy.com/en-us/mem/intune/apps/apps-win32-supersedence
Please note that if you manually installed the apps instead of deploying them via Intune, you cannot update them via Intune.
Moreover, here is a link about how to patch third part application.
https://patchmypc.com/third-party-patch-management-for-microsoft-intune
Non-official, just for reference.
Hope above information can be helpful.
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