I'm certainly no expert, but I can't see how applying more muscles to an effort wouldn't increase long distance efficiency. If you were to spin with only one leg, you certainly wouldn't be as efficient as spinning with the muscles of both legs (over both short and long distances). By increasing the number of muscles used you will decrease the load on any one muscle, thus slowing its fatigue and making it more efficient. There’d be no need to keep your output at your maximum level for long distances (no one’s cardio system can handle that), otherwise we’d all be sprinting entire centuries.

I experienced a gain in efficiency when I switched to clipless pedals (from nothing) but I can’t quantify that gain since I switched to clipless pedals when I bought my road bike (previously on a MTB) and there are just too many variables to isolate the pedals. Granted I would’ve seen huge gains just by changing bikes, but I could feel myself becoming more efficient with each ride as I became accustomed to spinning with the new pedals.