Yes, as Auto Zone can be thought of as just another Centrify Zone - but one where the user's UNIX Profile is automatically generated from Active Directory, so there is no configuration needed in the DirectManage/DirectControl console. It is effectively a "Ghost Zone".
Note that although the two Zone modes can co-exist, a user logging into a computer that is joined in Auto Zone mode may have a different UID and GID than when they log into a Zone Mode system. If the user needs to have the same UID and GID for all systems, then the Zone Mode needs to be configured to generate their UIDs and GIDs from the Active Directory SID, as this is the method that Auto Zone uses.
If a system is being moved from Auto Zone to Zone Mode, or vice versa, and the "Autogenerate from SID" has not been used, then Account Migration will need to be used to map the user's new UID over their old UID as recognised by the local system.