According to the javadoc the VelocityConfigurer has a setter for the resourceLoaderPath. The setter is inherited from the VelocityEngineFactory.
So it should be possible to set it:
@Bean
public VelocityConfigurer velocityConfig() {
VelocityConfigurer velocityConfigurer = new VelocityConfigurer();
velocityConfigurer.setResourceLoaderPath("/WEB-INF/velocity/");
return velocityConfigurer;
}