Do I get a free Group Policy Compliance Reporter license with my PolicyPak On-Prempurchase when using it with MDM ?

Yes, but those machines must be domain-joined and must be getting their directives from Group Policy, and not from MDM. Said another way, you can LICENSE your machines via the MDM method, but then join them to a domain, deploy Group Policy settings to them, and in that case, the PolicyPak Group Policy Compliance Reporter will work just fine to report upon GPOs and their contents.