@EnterpriseArchitect Thanks for posting in our Q&A.
Based on my understanding, users have M365 E3 or E5 license are enough. intune license is included in Microsoft 365 E5 and Microsoft 365 E3 licenses.
https://learn.microsoft.com/en-us/mem/intune/fundamentals/licenses#microsoft-intune-plan-1
If you want to deploy third-party software packages, it is suggested to use win32 app via intune.
https://learn.microsoft.com/en-us/mem/intune/apps/apps-win32-add
And we can add Win32 app supersedence to update this app.
https://learn.microsoft.com/en-us/mem/intune/apps/apps-win32-supersedence
Hope it will give you some ideas.
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