In org.apache.catalina.startup.Catalina.load()

// Replace System.out and System.err with a custom PrintStream
// TODO: move to Embedded, make it configurable
SystemLogHandler systemlog = new SystemLogHandler(System.out);
System.setOut(systemlog);
System.setErr(systemlog);

As the TODO suggests this need to be configurable so jbossweb-tomcatXX.sar can turn it off for Tomcat embedded in JBoss AS where System.err and System.out are controlled by Log4JService.