I haven't experienced the same issue. I do know that the .EXE installer will remove the Service entirely, if exists, and readds it anew. If you have a Group Policy preventing Services from being added as Automatic that could be the cause of it. Regardless, from an elevated cmd prompt you should be able to use

Set-Service -Name MailService -StartupType Automatic

I know the big one for me is always forgetting to set the Recovery Options to "Restart the Service" instead of "None" for 1st, 2nd, and Subsequent Failures every time I install an update. This always gets my goat about the SmarterMail installer!