No. It's indexed as it is extracted by Tika. But TBH I did not understand what is the problem. May be illustrate with an example what you have now and what you would like to see?
May be some enhancements need to be done in fscrawler project. For sure I should support adding easily memory settings to the fscrawler job. For now, you have to hack the script or set $JAVA_OPTS.
I opened Add FS_JAVA_OPTS JVM option · Issue #134 · dadoonet/fscrawler · GitHub for this. Feel free to contribute! 
I never tested it with Kibana for now. I'd advice that you first test with simple curl commands that everything has been indexed as expected. Is it the case?