The xsltfile parameter allows you to pass in your own XSL file for generating the HTML output.
<project>
...
<reporting>
<plugins>
<plugin>
<groupId>net.sf.jfxdplugin</groupId>
<artifactId>maven-javafxdoc-plugin</artifactId>
<version>1.0</version>
<configuration>
<xsltfile>${basedir}/src/main/xsl/mydoc.xsl</xsltfile>
</configuration>
</plugin>
</plugins>
...
</reporting>
...
</project>