I think that you need to look at the way the trannys are built. As Sparky says if you get rid of the torque converter you really help an automatic. An automatic is usually two sets of planetary gears, one in the case of a Powerglide, plus they need an oil pump to make things work. Planetary gear sets are typically 95 to 97% efficient, so in series that would make them 90 to 94% total plus the oil pump drive and the internal "windage" so it would be easy to have an automatic that was less than 90% over all efficiency. Maybe that's why transmission coolers are so popular with automatics.
Standard trannys, once they get into high gear, and if the tranny is not an over drive type, then the power is transferred from the main drive gear straight through the top shaft to the tail shaft and there are no gear meshes that are involved in transmitting the power. Whereas an over drive tranny requires that the power goes from the main drive input gear to the cluster(one gear mesh) and then from the cluster (counter shaft as some call it) through the over drive gear (a second gear mesh) and out the tail shaft. Each gear mesh is probably a 2-3% power loss. So I would vote for a manual trans without an overdrive top gear as the most efficient. There is also hp to be found in using thinner transmission fluid in a standard tranny but you need to dry sump it and do some oil spraying on the gears, but you can easily gain more than it takes to drive the oil pump.
Rex