This article should be made clearer.
".htaccess-style INI files" meant to me that the ini settings had to follow the syntax used in .htaccess, but this is not the case!
You have to use
php_flag register_globals on
Also, the changes can take a while to propagate to all processes if you have a long process time out.
Restarting php-fpm can give you an answer quicker :)