Your own words asked what happened when "exhaust backpressure" falls with increasing altitude, so clearly what happens at or beyond the exhaust port did matter.
Also, in your words:
On the exhaust stroke one cylinder's worth of volume is expelled. Volume past the exhaust valve doesn't equal volume past the intake, and it does depend on load. Your background in aerodynamics should be sufficient to understand the implications of compressible flow, local mach number, and temperature of a gas.
Your reduction seems to state that the volume of a cylinder is constant when the piston is at BDC. I would hope that wasn't contested.
In any case, have fun over there.