@Jack Fields, Thanks for posting in Q&A.
For your issues, here are some information you can refer.
1.For deploying apps via Intune, the msi file is the easiest way to deploy, and for the free convert .exe to msi, here is a tool you can refer.
https://apps.microsoft.com/detail/xp9cwggd5rxjwm?hl=en-US&gl=US
2.If you deploy apps via win32 and want to update them via Intune, you can add the update package to supersedence, here is an official document you can refer.
https://learn.microsoft.com/en-us/mem/intune/apps/apps-win32-supersedence
3.As for how/when Microsoft Store Apps send out updated versions, that depends on how/when the app developers will send out the updated versions, after they send out the latest app version, Microsoft Store will send out the latest app version, also you can pay attention to Microsoft Store which will provide the latest app update information.
Hope this can help you.
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