Why? The client can work pretty well with the --webroot issue method on any webserver. Hell, if you can take your webserver offline for a short time you can use the --standalone option's built in server.

Even where you webroot is wired into something else (a proxy, fastcgi, uwsgi/django, etc), you can rig it to try to see if a file exists in another directory before handing off.

    location / {
        root /web/$site/webroot;
        try_files $uri $uri/ @django;
        access_log off;
    }

    location @django {
        include uwsgi_params;
        uwsgi_pass unix:/web/$site/socket;
    }

Simple! I reuse this in many sites (hence the $site variable) but you could decouple this and use a single directory for all sites/certificates (it doesn't have to be in the webroot, just something nginx can read).