This link tells it all:
http://www.cisco.com/en/US/partner/docs/voice_ip_comm/cucimoc/8_5/english/installguide/config_active_directory.html
The reg file you have -- which contains the Policies branch -- is supposed to be pushed and managed via GPO. If you're manually deploying via batch or script, you'll be using the alternate path (without the Policies branch)
From the CCO Downloads page for CUCI-Lync, you can download the admin files which contain the GPO. As always with AD, there are numerous ways to go about it from there.
Alternatively, you can use a package management tool or a login script to write the files to registry.
The caveat is that these settings are contained within the Current User registry, so an admin can't push a batch file remotely; and many users may not have privileges to write files to the registry.
If your environment is set up such that loading the reg entries via script or batch is easiest, do that. If not do a GPO