When the piston is moving upwards the space below it that it vacates is where the gas has to flow to. Most of it comes from the inlet so to minimize losses the inlet should be aimed at this space.
Secondary flow into this space also comes out of the crankcase and transfer passages. We want to minimize this last one and one way to do this is to lower the primary compression ratio - one often forgotten secondary effect of large case volumes. Often the side effect of the Boyesen ports is just that, rather than flow out of the transfer passages the flow is out of the inlet cavity which promotes reed opening.
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