You can try generating a new BOM entry based on your JRE XOM and containing the classes responsible for the warnings:
Launch the 'New BOM Entry' wizard (File -> New -> BOM Entry in the Rules perspective).
In the first page of the 'New BOM Entry' wizard click 'Next >' (the option 'Create a BOM entry from a XOM' should be selected by default).
In the second page of the 'New BOM Entry' wizard, click on the 'Browse XOM...' button. The 'Browse XOM' dialog should pop-up.
In the 'Browse XOM' dialog, select the entry corresponding to your JRE, then click 'OK'.
- In the 'New BOM Entry' wizard, tick the classes you are interested in, then click 'Finish'.
Note that it worked fine for me for java.util.UUID but I suspect that depending of which classes and members are imported into your BOM entry, you could end-up with other (lots of?) similar warnings.
Unfortunately, I didn't find any other way to get rid of those...