After setting all the Options and environment variables in netbeans.conf, nbactions.xml, as a global environment variable, catalina.bat etc I still couldn't pass the VM options to the registered Tomcat server untill today I realised that, it's in the same place as you register the server!!!
And this took me ages to figure out (yea, daft me! ) so I'm sharing it here for my own reference and for anyone who runs into this.

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