You are actually correct - Lugs are supposed to be torqued Clean & Dry.
Wish you were wrong, and that lubricated was the standard - it would avoid so many of the corrosion issues that make repair difficult & expensive.
The days of "Grease is cheaper than bearings, so use plenty" are long gone. That quote is from the Model T era, and I don't know how long it lasted past that. Using the minimum necessary saves $, and isn't often an issue during warranty.
Corroded fasteners need more torque to tighten properly, lubricated need less, crossing fingers a bit & lubricating corroded fasteners seems to work in practice.
Avoiding over-torque becomes more important, I've seen 20% as a recommended reduction on clean fasteners. Gets into judgement calls on re-use of fasteners at all sometimes.
Nice clean Engine components aren't an issue (head, crank as you mentioned). Spark plugs can be, steel into aluminum is the worst & almost universal currently.
Never-Seize has been wonderful whenever I chose to use it, brakes that work for years instead of giving trouble is just one example.
Guess it depends on circumstances. In a salt corrosion environment it can save a lot of grief.
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