okrampf if you made changes in map-wp-fastcgi-cache.conf, just create an empty file map-wp-fastcgi-cache.conf.custom to make sure WordOps will not overwrite this file.
touch /etc/nginx/conf.d/map-wp-fastcgi-cache.conf.custom
Instead, WordOps will create a new file map-wp-fastcgi-cache.conf.orig, this you will be able to easily check if there are changes and to add them into your conf.
But currently there is no way to add a specific configuration per site, because map directives should be defined inside the http {} block.