After installing the Internet Explorer 11 adm template, the Enterprise Mode settings are missing from the GPO. If you find Enterprise Mode settings missing from the IE 11 GPO, Microsoft say that this is because:
You had the Group Policy Management Tool open when you copied in the IE 11 adm template
Another reason that Enterprise Mode is missing from the group policy after importing the IE 11 ADM template, could be that you are not running the Group Policy Management Tools from a Windows 8.1 or Server 2012 member server or that you don’t have a sufficient patch level of IE 11 on the PC you are managing GPOs from.
❗ Note: IE 11 Enterprise Mode requires version: 11.0.9600.17358, update verions: 11.0.13 (KB2987107). Also, IE 11 Enterprise Mode does not work with IE 11 RTM version.