I filed this bug a few times using Apple Feedback since updating to El Capitan. Last month though, I filed a Bug Report and an Apple Engineer contacted me for more information. I ran a Terminal report for him. Then he came back and told me that my Bug Report was a duplicate and that was the end of it.
One of the strange things is that in my Mail Preferences>Accounts>Advanced>"Automatically detect and maintain account settings" is greyed out for my Gmail Accounts so I can't uncheck that. It's not greyed out for my iCloud account. I read that unchecking this setting could be a fix.
I tried a fix for the greyed out option by deleting my Gmail accounts in V3. Then in the Mail Data folder, I deleted the three files that have Envelope in the name, and in User Library>Containers I moved the com.apple.mail folder into the trash. After that, it's still greyed out and I still get auto launch. I've exhausted every avenue and given up now. I keep my MacBook Pro clean and always fix any bugs after upgrades, but this one truly baffles me.