nginx_vhost.conf.master wrong ssl path
I think there is a bug inside the template, because the ssl section has the following lines:
ssl_certificate <tmpl_var name='document_root'>/ssl/<tmpl_var name='ssl_domain'>.crt;
ssl_certificate_key <tmpl_var name='document_root'>/ssl/<tmpl_var name='ssl_domain'>.key;
But only for redirects! In "normal" webservers are ssl settings correct:
ssl_certificate <tmpl_var name='ssl_crt_file'>;
ssl_certificate_key <tmpl_var name='ssl_key_file'>;
So i think the rewrites should be patched to make letsencrypt possible ;) Otherwise the $domain-le.crt files will not be found.