Hey everyone I worked extensively with Microsoft on the Lync machine level Plist issues and we were able to resolve them.
Here is the basics.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>Backward_Compatible_Version</key>
<integer>1</integer>
<key>Current_Version</key>
<integer>1</integer>
<key>hkey_local_machine</key>
<string><<MacRegNoValue>></string>
<key>hkey_local_machinesoftware</key>
<string><<MacRegNoValue>></string>
<key>hkey_local_machinesoftwarepolicies</key>
<string><<MacRegNoValue>></string>
<key>hkey_local_machinesoftwarepoliciesmicrosoft</key>
<string><<MacRegNoValue>></string>
<key>hkey_local_machinesoftwarepoliciesmicrosoftcommunicator</key>
<string><<MacRegNoValue>></string>
<key>hkey_local_machinesoftwarepoliciesmicrosoftcommunicatorconfigurationmode</key>
<integer>1</integer>
<key>hkey_local_machinesoftwarepoliciesmicrosoftcommunicatorserveraddressinternal</key>
<string>domain.com</string>
<key>hkey_local_machinesoftwarepoliciesmicrosoftcommunicatorserveraddressexternal</key>
<string>domain.com</string>
</dict>
</plist>