We do use DEP on our OS X machines
Since 9.96 there are new options in PreStage Enrolments:
Selected items are not displayed in the Setup Assistant during enrollment
...Touch ID... etc.
And "FileVault" seems to be interlinked with the tab "Account Settings":
When you choose "Additional administrator Accounts" the option "Filevault" is not available anymore.
Could anyone share more insights to these dependencies?