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Windchill supports only the version of the Tomcat it comes with. It does not support other versions, nor other distributions of the same version of Tomcat.
For a given release stream one can run the version of Tomcat from any MOR level with any other MOR level. For instance, you don't have to update to the latest Tomcat when moving to a new MOR (though this is recommended, of course). You can also move to the Tomcat from a newer MOR without moving other components to the newer MOR. The same is true for Apache.