DNS won't be an issue as all client agent communication is client agent initiated (remote control, WoL, and client push are kind of exceptions to this statement but they aren't really part of the agent itself). Your issue will be that ConfigMgr simply
requires unique NetBIOS names for managed Windows systems. This is a leftover requirement from way back that still unfortunately exists to my knowledge.
Jason | http://blog.configmgrftw.com | @jasonsandys