So we are really back to the guidance I always give people. Buy the automatic transmission for luxury. Buy the manual transmission for better performance and better mileage. This rule really hasn't changed for the past 60 years.
Every few years, Consumer Reports tests a group of cars that are "identical twins". Each "twin" has one car that is MT, and the other that is AT. Otherwise, they are as similar as possible. They try to get a sampling of various types of cars (sports cars, economy cars, etc.). The car with the MT virtually always has better acceleration and better mileage than the identical car with the AT. Other testing organizations report similar results.
In terms of the EPA ratings, it is important to remember these tests are conducted under laboratory conditions, not real world driving. Many people with AT cars complain their cars do not achieve the EPA ratings. Most people with MT cars get fairly close to the EPA numbers. I am a bit surprised the new EPA 328i rating shows the MT version getting better mileage than the AT version. Maybe a dose of reality?
Sorry, an automatic is still an automatic, regardless of how many speeds it contains. I am using the term automatic to mean a transmission that has a torque converter. This does not include the automated manual transmissions.