I think we can safely overlook any difference in diesel engine overall efficiency- even if there IS a difference, it would be minimal in my opinion, perhaps one or two percent. I'm fairly sure that the different mileage per ton is due to the much larger auxiliary electrical load of the US subs, though I don't have any figures for the power consumption of the auxiliary systems for either IXD2 or Gato unfortunately.
Interesting read by Dieter Hille, by the way!
The story about the Malays duplicating a crack in a newly-made bearing is probably quite true- I had a somewhat similar experience in Singapore in the 1970s. The tanker I was serving in required a new section of piping in the deck steam line, so the Chief Engineer arranged for a foreman from one of the local engineering firms to measure the old section. Soon enough two old Chinese men from the engineering firm appeared; the Chief showed them the section to be replaced and instructed them to "Make new pipe same-same old pipe" to which they replied "Yes, Chief, no problem", then proceeded to measure the section with a piece of string (!!!) which one of them happened to have in his pocket.
The next morning a team arrived with the newly-made section of piping, which was a perfect drop-in fit. However.... they had also copied EVERY SINGLE dent, twist and other imperfection- except for the long crack which was the reason for the old section's replacement. Not unnaturally, the Chief was livid, but the foreman said "Chief, you speak make new pipe same-same old pipe, we make new pipe same-same old pipe". In the end the Chief had to sign for work carried out.