I understand that the Oracle Java SE contains closed source extensions and tools that are not part of the OpenJDK however is the Oracle Java SE JVM identical to the OpenJDK JVM or does Oracle make changes to the OpenJDK JVM before releasing it as a Java SE JVM?
Update 1: I found some info from the JDK7 updates projects: http://openjdk.java.net/projects/jdk7u/qanda.html
Will the 7 Update Project receive security fixes from Oracle?
Yes.
As with OpenJDK 6, security fixes are first kept confidential and applied to a private forest before being pushed to the public forest as part of the general synchronized publication of the fix to effected JDK release trains. In addition, they will not go through the public code review and putback approval process, and their corresponding issues in the Project's issue tracker will not be publicly visible.