Intune_Support_Team sorry for the very late reply. We figured out the scenario where an Azure AD registered Windows computer ends up with the same Intune Device ID and the Azure AD Device ID. It happened when there is already an account configured for another tenant under "Access work or school". Intune enrollment was done using Company portal application. This resulted in the problem I described earlier.
There is another scenario where a Mac computer ends up with the same Intune Device ID and the Azure AD Device ID. It happened when the user account used to enroll the computer has the "Device enrollment managers" role in Intune. This does not seem to affect the Conditional Access as it did for the Windows computer as there is only one device account created in Azure AD.