According to http://docs.oracle.com/javafx/2/deployment/self-contained-packaging.htm:
To add a custom UI to the MSI package, you can customize WiX template file used by JavaFX Packager using technique from 6.2.4. Consult WiX documentation for more details.
Assuming I figure out how to create a custom template file, how do I pass it into the JavaFX Maven Plugin?
When native package is created with the help of javafx-maven-plugin(2.0) we have to mention the icon for application in main/deploy/package/windows/demo.ico then the icon present in the deploy directory added to classpath like that if wix template is added in deploy directory then it might be possible that the wix template is available at classpath.
Then this wix script may be use by javafxpackager like the icon is use.ultimately the javafx plugin uses the javafxpackager internally.