Got the official word from Maxon regarding Cinema 4D R12 and the new licensing scheme:
"Beginning with Release 12, customers need to obtain a Command Line license from us (Maxon), which is served via the License Server and enables command-line rendering. As of right now, we (Maxon) aren't and don't plan to charge for Command Line licenses (at least for customers in North and South America - I'm not sure what the policy is in other regions). Customers can contact their Maxon sales rep or reseller to get a command line license - by default they'll be provided with a 25-seat capability."