Please feel free to mark this as solved. Ill write a seperate thread to document the centmindmod guide but for anyone reading here is how I fixed it :
In the working version : Root has been specified as /home2/nginx/domains/workingdomain.com/public/public
Working version SomeDomain.conf :
https://pastebin.com/DVXKYR6J
The duplicated public isnt really a duplicate. Its just it dumps the non secured stuff in there. I could not for the life of me get it to work when I moved the /public/public to /public and changed every variable known to man in the config files.
The addition of these little lines in the workingdomain.conf file
https://pastebin.com/3t023Ztb
Thanks all for your time.
Andy