Further to my previous post, after a bit of playing around I’ve found a solution to the problem of using Exchange aliases in OS X Mail under OS X 10.11 El Capitan.
It seems the accounts.plist file is now superfluous and the way to add an alias is as follows:
1. In OSX Mail, select Mail -> Preferences.
2. Highlight your Exchange account from the list on the left.
3. Make sure the Account Information tab is selected in the right panel and look for the Alias dropdown.
4. The alias dropdown may be greyed out (it was for me) so, if it is, go to the Outgoing Mail Server dropdown and change it to none.
5. Close down that panel (or select another mail account from the left menu if you have one) to force it to save. It should ask you if you want to save settings.
6. Go back into that panel and you should find the Alias dropdown is no longer greyed out, so click the dropdown box and then select Edit Aliases.
7. You can now use the + and – buttons to add any aliases you want.
8. When you’ve added all your aliases, before you exit, change the Outgoing Mail Server entry back to Exchange.
That’s it. You shouldn’t even need to reboot the mail app. Your aliases should now be available to select via the ‘From‘ dropdown when you create or reply to a mail message.