Move the intake valves from the cylinder heads to the piston crowns. The transplanted valves will rely solely on momentum and pressure differential to operate¹. The crankcase is now the intake manifold². A one-way valve on the crankcase is now the throttle.
Changing the strength of the constrictor
[edit: I suppose defining 'constrictor' would help : it's just a flap valve on the crankcase, letting air in] changes the amount of air sucked into the crankcase when both pistons simultaneously head up to TDC, thus changing the amount of air that will be pushed into³ whichever cylinder has its intake valve open when they both head down to BDC.
That's supercharging. Limiting the amount of inducted air to less than one cylinder's worth results in subcharging, useful for creating an Atkinson-type of cycle.
The end result is an engine that can segue from para-Atkinson operation to "supercharged powerhouse" pretty smoothly. It's not magical - the geometric compression ratio is fixed and supercharging ain't free - but the much wider range of aspiration is accomplished with no added complexity (some removed, as a matter of fact).
¹ Vacuum operated intake valves are common enough, but momentum - where the valve wants to keep moving when the piston slows down after the midpoint of travel - not only mitigates valve float (where the valve action can't keep up at high speeds) but may even introduce the opposite problem, where they want to open or shut too early.
² but not a carburetor. Nothing wrong with carburetion, but for the purpose of this post we'll stick with direct injection, inside the cylinder.
³ "pushed" because, unlike any other multicylinder engine, a 4st 2cyl has all the cylinders moving up and down at the same time. Not only is the crankcase a pump because of this, but it's pumping more than 1 cylinder's worth at a time. This is sortof the main point of the post: making use of that.