We used to create IzPack 4.3.5 installers containing a JDK as part of the installed product. For the installation process itself we provided a copy of the JDK on the install medium.
With IzPack 4.3.5 the uninstaller worked 'good enough'. While it was not removing the JDK packed with the product and used to run the uninstaller, we were able to simply provide a start script for the uninstaller to remove the remaining JDK and base directories via OS commands after the uninstaller returned.
With IzPack 5.1.3 (and 5.1.4-SNAPSHOT-f390e) the uninstaller tries to remove the JDK packed with the product and used to run it - and fails (without showing an error message) after removing some of the JDK files. Most of the product files are left on disk. On Windows, Start Menu entries are not removed.