I think the increased efficiency is caused by the reduced shear zone. Slower air from the big bypass causes less shear when meeting the outside ambient air at the back of the engine. Should the bypass not exist, a pure jet will cause rapidly moving air (much hotter too) to shear with the relatively static ambient air. In other words, air flow around the back of the engine is smoother.
Noise is much less on a bypass engine too. Probably for the same reason.
There may of course be other reasons for the increased efficiency, I could only remember this one.