JPA configuration should support configurationfile as a way to do overrides the persistence.xml location, like:

<target name="hbm2ddl">
<hibernatetool destdir="${src-hbmtools.dir}">
<jpaconfiguration configurationfile="META-INF/${database}/persistence.xml"/>
<classpath location="${build.classes.dir}"/>
<hbm2ddl export="false" outputfilename="${module.name}.ddl" format="true" haltonerror="true"/>
</hibernatetool>
</target>

When I try it, I got "<jpaconfiguration> currently only support autodiscovery from META-INF/persistence.xml. Thus setting the configurationfile attribute is not allowed"