The WinExeBundler.java Bundler class is not copying the project-name.iss drop in resource (package/windows/project-name.iss) to the temporary win-image directory. So the default template.iss file is always used instead and the inno setup project cannot be configured.

I believe in WinExeBundler.prepareMainProjectFile before calling preprocessTextResource for the iss file, fetchResource needs to be called to copy the drop-in resource from the package folder to the win-image temporary folder where preprocessTextResource looks for files.

Workaround:

<!-- Copy the ant-javafx.jar -->
<copy file="${ant.lib}/ant-javafx.jar" toFile="ant-javafx-patched.jar" />

<!-- Patch it with our Inno Setup project file -->
<jar destfile="ant-javafx-patched.jar" update="true">
<zipfileset file="package/windows/${project.name}.iss" fullpath="com/sun/javafx/tools/resource/windows/template.iss" />
</jar>

<!-- Now define the javafx ant tasks using our patched jar -->
<!-- Don't forget to include '.' in the classpath -->
<taskdef
resource="com/sun/javafx/tools/ant/antlib.xml"
uri="javafx:com.sun.javafx.tools.ant"
classpath=".:ant-javafx-patched.jar" />