It should help either way. If the valves are closed at TDC, there will be a vacuum to overcome on the downstroke, but that same vacuum will pull the piston back up with equal force on the upstroke. Conversely, if they're closed at BDC, air pressure will create resistance on the upstroke, but it will push the piston back down on the downstroke. My bet is on vacuum being slightly better, because you'll have less heat lost through the cylinder walls if there's less air, but that might be negligible in the grand scheme.
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