What we are observing is if you use <exclude-unlisted-classes>true</exclude-unlisted-classes> in a persistence unit and then configure JPA in Spring like the markup shown below the persistence unit shows up fine in the IntelliJ Persistence Tool Window but the exlude-unlisted-classes is not honored and every class annotated with @Entity is visible under the persistence unit in the tool window. The same behavior exists in 12. I created an issue for it (http://youtrack.jetbrains.com/issue/IDEA-117612).
<bean id="..." class="org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean">
<property name="dataSource" ref="..." />
<property name="jpaVendorAdapter">
<bean class="org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter">
<property name="databasePlatform" value="org.hibernate.dialect.Oracle10gDialect" />
<property name="showSql" value="..." />
</bean>
</property>
<property name="jpaPropertyMap">
<map>
<!-- <entry key="hibernate.connection.autocommit" value="false"/>-->
<entry key="hibernate.max_fetch_depth" value="..." />
<entry key="hibernate.show_sql" value="..." />
</map>
</property>
<property name="persistenceUnitName" value="..." />
</bean>