I'm certain those contribute. A piston acting as an air spring with closed valves still has friction, and it will undoubtedly affect an exhaust not tuned for it. I'm nowhere near an expert on the matter, just someone who reads crap on the internet, but it stands to reason.
I think it would be neat to see a pair of 2 cylinder engines mated together at the crank with a clutch in between, so half of the engine could be truly deactivated.
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