Ideally, there should be a profile for the standard Java 7 API, and then profiles for each of the implementations with their classes. Of course extending the Java 7 profile.
The problem is that there are slight differences between every update of JRE/JDK (e.g. 12 classes were removed and 47 classes were added in rt.jar between 7u21 and 7u25).
You risk ending up with as many profiles as there are updates.
The difference between Windows and U*X in Java 7 rt.jar is about 1200 classes (900 for GUI - AWT/Swing/font/2D, 200 for IO - filesystem stuff, the rest for the differences in process/network/security implementation).
The difference between U*X'es is minimal, mostly security details and differences in process implementation.
One may perhaps create a "standard API" profile, a "generic internal API" profile and a "platform-specific internal API" profile (a use of which would perhaps set ReportStatus to ABOMINABLE)?
The important stuff are the java. and the javax. stuff. The rest can be bundled in their own profile which extends the JDK7 one.
And I wouldn't worry too much about changes between patch releases - creating a profile based on the latest available release is good enough IMHO.