So i sat through Apples tech update today where they spoke about the death of monolithic imaging. The reason this will not work with APFS volumes boils down to the fact that in order to update a system to High Sierra, the installer physically updates the machines firmware in order to support the new file system. That being said, one way around this (as promoted by Apple at this event) was to go back to the old NetInstall method. So in theory, clonedeploy could be used to mimic Apple NetInstall instead of Netboot in order to do an actual install of the OS which in turn will trigger the firmware update install on the client. After the install i would think it would be possible for clonedeploy to THEN install an MDM/Munki agent in order to pull down the apps needed? I'm not saying this would happen anytime soon as we all know you are super busy, but i just wanted to give you some insight into my takeaway from the event today in hopes it saves you some time and research.