Here's the code that prevents discovery:

        if (null == processInfo.getExecutable()) {
            log.debug("Ignoring Tomcat instance (agent may not be owner) with following command line: "
                + Arrays.toString(commandLine));
            return null;
        }

I think we can figure out another way to get the information provided by processInfo.getExecutable() and any other protected process info we currently rely on.