I did some digging around to find out how the Java Development Tools (JDT) project contributes the Java Preference options here. And I found that the extension point "org.eclipse.ui.preferenceTransfer" is actually the one that we need to extend in order to define new preference kinds to export. The following snippet is taken from org.eclipse.jdt.ui project's plugin.xml file:
So if you have new preference kinds you want to export, this is the way to go. You can also peek into JDT/UI's plugin file to explore further.