Sorry, but Webinoly doesn't have native support for individual PHP sockets and users for each site.
Sometimes (not always) Webinoly overwrite conf files during the update process. You can safely have you own custom nginx conf file located at /var/www/domain.com and it will not be overwritted.
Read this ticket for more info - https://webinoly.com/support/313/nginx-configuration-for-woocommerce
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