You can enter the URL with port number in the address bar, for example: ftp://servername:10021/index.html
But the FTP upload/download dialog does not support this yet, but it will work in the next version. Then you can enter servername:port in the "Server name" field.
I said it _will_ work in the next version, i.e. 3.8.2, which is not yet released. You may want to subscribe the newsletter to be the first to get the new version.