Solved
If you don't have -Djava.library.path set then Thingworx normally crashes
Also keep in mind that if you have spaces in the path, you should put it into quotes, like
set JAVA_OPTS=-Dserver -Dd64 -XX:+UseG1GC -Dfile.encoding=UTF-8 -Djava.library.path="c:\Program Files (x86)\Apache Foundation\Apache Tomcat\webapps\WEB-INF"
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