I’m not using Mail.app on OS X these days (opted for MailMate), but I received an email from Mathias Törnblom updating the database vacuuming trick I’d posted previously. It makes the script work for Mail on El Capitan, and maintains backward compatibility.
This is a companion discussion topic for the original entry at https://brettterpstra.com/2015/10/27/vacuuming-mail-dot-app-on-el-capitan