This is the go to source for VMM. Can VMM do x? How do you make VMM do x? Both questions answered in this ~800 page document, with a multitude of links to related information. Keep this one in your VMM toolkit.
… and to answer your first question, yes; SC2012_VMM does not reflect that there is updated R2 material. This is the right doc.
System Center 2012 – Virtual Machine Manager
System Center 2012 Service Pack 1 (SP1) – Virtual Machine Manager (VMM)
System Center 2012 R2 Virtual Machine Manager – NICE!
Word and PDF versions available.
Very good documentation.
Chapter Ports & Protocols for VMM is missing two communication types:
SCVMM to Hyper-V Hosts (445 -> VMM Agent Push Installation)
SCVMM to SMB3 File Server (445 -> Periodic Access Verification )