@Djordje Novakovic Thanks for posting in our Q&A.
Yes. The user can't install apps from Apple store using managed Apple ID.
We can deploy apps via intune. Intune supports MacOS app type is intune following:
https://learn.microsoft.com/en-us/mem/intune/apps/apps-add
Or we purchase apps through Apple Business Manager and assign volume-purchased apps to devices.
https://learn.microsoft.com/en-us/mem/intune/apps/vpp-apps-ios
If you want to assign other apps, line-of-business app is an option. However, the app file is needed to be a .pkg file.
https://learn.microsoft.com/en-us/mem/intune/apps/lob-apps-macos
Hope it will give you some ideas.
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