postfix: warning: /etc/postfix/main.cf, line 690: overriding earlier entry: config_directory=/etc/postfix
I have the same problem using postfix reload in Yosemite server, with the same error. Postfix is running, however, and I can restart it by using the GUI in server.

Sierra's postfix config files are, in fact, in  /Library/Server/Mail/Config/postfix/ and the files in /etc/postfix are not used and obsolete. Changing files in /etc/postfix won't do you any good. The file you need to sort out is /Library/Server/Mail/Config/postfix/main.cf