Lookup Metadata Column and Office 2016 Microsoft case # 118020817613809
Custom content types with lookup columns don't currently work in Office 2016 and SharePoint Server 2016. The lookup column data is not accessible from Office, so the metadata cannot be selected. This is not an issue with SharePoint online and Office 2016, or with SharePoint Server 2016 and Office 2013. This has been an issue that has been brought to Microsoft's attention going back a couple of years, and there is still no resolution.