The multi-instance support for tomcat needs to be completely re-done. Starting the the init script, which should always be installed by portage. Then any instance should symlink to the init script such as tomcat-*.instance -> tomcat-*.
Furthermore when you initially install tomcat, nothing more should be required. You should not have to run the instance manager to create the initial/default instance. It should work just by starting tomcat via init script after installation. Then for any additional instances, you can run the instance manger to create those as needed.
Ideally all instances can be tracked so most files are removed when tomcat is removed, and/or upgraded to a newer version. Right now because the instance manager creates directories and installs files completely outside of portage. You are left with a mess you must deal with manually.
The instance manager was really not done properly per the gentoo way of doing things. Not to mention it creates and leaves many more files and directories not under portage control. Really not good all around and needs to be redone entirely.
Submitted PR with my attempt to rework multi instance support: https://github.com/gentoo/gentoo/pull/1358