How about adding pre-installed apps as Windows Store apps to the VPP token and assign to users? Either Facetime or Contact can be found in Apple Store and should be assigned to a volume-purchased app.
By the way, Apple recently changed from using the Apple Device Enrollment Program (DEP) to using Apple Automated Device Enrollment (ADE). The Microsoft Intune user interface doesn't currently reflect that change. Currently, you'll still see Device Enrollment Program in the Intune portal. Wherever you see references to DEP, Intune now uses Automated Device Enrollment.
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