Can’t set JPA naming strategy after configuring multiple data sources (Spring 1.4.1 / Hibernate 5.x)

I had the same problem and fixed it with the following code (adapted to the code in the question – for a single entity manager):

protected Map<String, Object> jpaProperties() {
    Map<String, Object> props = new HashMap<>();
    props.put("hibernate.physical_naming_strategy", SpringPhysicalNamingStrategy.class.getName());
    props.put("hibernate.implicit_naming_strategy", SpringImplicitNamingStrategy.class.getName());
    return props;
}

@Primary
@Bean(name = "defaultEntityManager")
public LocalContainerEntityManagerFactoryBean defaultEntityManagerFactory(
    EntityManagerFactoryBuilder builder) {
    return builder
        .dataSource(auntDataSource())
        .packages(Aunt.class)
        .persistenceUnit("aunt")
        .properties(jpaProperties())
        .build();
}