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Checking my last adop sessions, I will answer your questions:
1. Cutover phase does not appear to run autoconfig. I recommend running adop with options=nodatabaseportion on the DMZ node first then apply on the internal node.
2. Prepare phase does run autoconfig on the patch filesystem
3. I do not recommend using noautoconfig option as that is an apply option anyway
4. fs_clone clones the new run patch filesystem to the patch filesystem.
Oracle E-Business Suite Release 12.2: Online Patching FAQ (Doc ID 1583902.1)