With SCCM 2012 R2 SP1 there are several changes (here other blog article)
About mobile management consider that both Microsoft Intune and Configuration Manager 2012 have the same Mobile Device Management features now. More on the new features in later blogs, today I want to focus on the Mobile Application Management Policies in Configuration Manager 2012 R2 SP1.
In this specific case it would reappear Application Management Policies:
here is an example screenshot, in this node you are able to create the Mobile Application Management Policies for Android and Apple iOS Apps and Managed Browsers. The key point is that you can create a policy for managed browsers and applications and configure the same settings as in Microsoft Intune stand alone.
http://configmgrblog.com/2015/05/17/mobile-application-management-support-arrived-in-configmgr-2012/