Locking Torque converters have been the rule for a LONG time, like since the 70's... With all due respect for the guys from Car Talk, this *helps* with the efficiency, but there still is some energy losses due to the necessity of running the automatic part of the transmission. You have to keep the shift clutches engaged, that takes hydraulic pressure which implies a pump is running someplace. You also must circulate the transmission fluid to keep the various things lubricated and cool, which takes some power too. Power consumption in the transmission means less power for driving getting to the wheels.
I'm not saying the differential between the automatic and the manual is all that much these days, it's not, but if you are on the highway the manual is going to be better. Now if you want to argue that it's unlikely that your average skilled driver would be able to achieve better gas mileage in a mixed environment of city and highway driving on their manual, that for 99.9% of drivers would do better on an automatic, I can only agree with you. However, just straight out driving down the road at highway speed, not shifting, that manual is going to be hard to beat, all things being equal.
Of course things are rarely equal. For example (outside of big rig trucks) manual transmissions seem to top out at 6 gears, while most automatics are now at least 7 with some having 8, or even 9 gears. (A far cry from the old 3 speed automatics).
That gives a better chance that the automatic can select a more ideal gear ratio for your speed than the manual. Potentially having the engine at a better RPM could more than offset the parasitic losses of the automatic transmission.