I was recently involved in the setup of a shared management infrastructure based on system center configuration manager 2012 R2. Now this has proven to be challenging so I share some of the leassons learned :
The following blog explaings cross forest support in config manager : http://blogs.technet.com/b/neilp/archive/2012/08/20/cross-forest-support-in-system-center-2012-configuration-manager-part-1.aspx.
You can use AD Sites as boundaries. The site names need to be unique but modifying an AD Site name normally has no impact.
Deployment using group policy together with a set of adm templates is an efficient deployment method. No special firewall requirements and all active machines recieve the sccm client. No discovery methods needed.
Proxy management Points.
Secondary sites with management point are not always used , some actions require the client to contact the assigned management point. See https://technet.microsoft.com/en-us/library/bb632435.aspx. Since the clients are not in the same ad forest and ad has not been extended, they will contact their assigned management point first.
OSD and AD site boundaries
WinPE is not domain joined and will not be able to use ad site boundaries. See http://blogs.msdn.com/b/chrissu/archive/2014/06/21/workgroup-clients.aspx