If you are not wedded to the paradigm of having 3 separate persistence.xml files and copying one or the other selectively, you can use maven profiles with filtering like this (just implemented this the other day and today came across your post):
In persistence.xml:
<property name="hibernate.show_sql" value="${hibernate.debug}" />
<property name="hibernate.format_sql" value="${hibernate.debug}" />
In pom.xml create a profile and define the variable:
<profiles>
<profile>
<id>hib-debug</id>
<properties>
<hibernate.debug>true</hibernate.debug>
</properties>
</profile>
</profiles>
define a default for when you build without specifying a profile:
<properties>
<hibernate.debug>false</hibernate.debug>
</properties>
and.... make sure you turn on resource filtering:
<resources>
<resource>
<directory>src/main/resources</directory>
<filtering>true</filtering>
</resource>
</resources>
Then you build with mvn -Phib-debug and voila! Substitution is done.