The update has still not addressed the issue with the smtp servers not saving to individual accounts.
Following the 10.11.1 update I still cannot send mail, although the blank server bug has been fixed, when I select an SMTP server it applies that change to all email accounts on the Macbook. When I try to send it brings up the server selection dialog, but it still won't send. I have unchecked all the check boxes about automatically updating settings on the accounts and SMTP servers, but no luck so far. I'm running on a late 2008 MBP.
MacBook Pro, OS X El Capitan (10.11.1)