We have performed extensive testing with the SEPM (and changed the way certain features work) to fix some issues prior to RU6, but if you believe there is still an issue with the SEPM then please feel free to contact secure@symantec.com with your concerns and they will work with our engineering and PM team to determine if there is a problem and then get it fixed.
It could be a case that the version of tomcat we are using has known issues, but only in certain modules, which we probably aren't using. Bear in mind that 9090 and 8443 have always been in use, and apart from hosting new services in RU6 onwards, the versions, etc. haven't changed.