I managed to figure it out with some digging and testing.
First I included the IE Personal Settings config file from Windows Common Settings but that did not capture the users plugin settings choice.
I had to add HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Ext\Settings to the list of included registry trees to capture the users choices for all plugins.
You can capture a specific plugin by specifying HKCU\SOFTWARE\Microsoft\Windows\CurrentVersion\Ext\Settings\<CLSID of the plugin>
