By default, in 2012(R2), it is not possible to use the same RDS Host Server to publish both RemoteApps and full remote desktops. This is because a RDS server can only be part of one and only one Session Collection, and a Session Collection can only either publish remote desktops or RemoteApps.

But there is an "unofficial and very unsupported" workaround which allows you to publish the full desktop in addition to the RemoteApps from the same Collection. This can be achieved by manually toggle publishing through the registry on the server running the RD Broker/Gateway.

1. Using regedit, navigate to the key:
   HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Terminal Server\ CentralPublishedResources\PublishedFarms\<collection name>\RemoteDesktops\<collection name>
   Note: replace collection name accordingly.
2. In there, set the value of ShowInPortal (REG_DWORD) to 0x00000001.

The change does not require a reboot.