@Federico Coppola , From your description, it seems we enroll iOS devices into Intune by using Apple's Automated Device Enrollment. If there's any misunderstanding, please let us know.
For corporate devices we usually don't assign the Company Portal app from the app store directly on ADE-enrolled devices. But we provision it through ADE as an VPP app so it will be installed after default iOS configuration. We can see more details in the following link:
From my point of view, Microsoft Intune Company Portal is needed. We can deploy it as an VPP app.
Hope it can help.
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