Modern lock-up torque converters and overdrive gear(s) have taken away much of the fuel mileage advantage that manual transmissions once had... I have seen some applications where the TC locks just above idle and stays locked until you come to a stop again acting just like a clutch and eliminating much of the hydraulic pumping loss of the automatic transmissions of yesteryear that were basically "slipping" 100% of the time. My guess is that GM is offering the manual transmission diesel just to woo VW TDI prior owners, but the take rate will still be very low...With that crazy 9-speed auto with a ridiculous number of gears to pick from, the auto will probably end up with the higher EPA sticker for city/combined. Somehow, despite the manual 2016 gasser having a taller 6th gear, the automatic gets the higher EPA rating.
In the real-world - it may end up being very close!
in one of the recent car mags, there was a discussion about how most new automatic transmissions with their large number of gears actually do better than manuals in mpg return. In fact, most modern manuals have gears 5 & 6 as over drives , leaving the lower gears for acceleration/ performance. A 10 speed auto offers the manufacturer a whole lot of more options for performance and fuel economy.This article hints at it with the manual transmission. I think it's very doable.
Chevrolet Cruze Diesel's Mileage Potential Is All in the Gearing