I'm hardly an automotive expert, but from what I understand, (1) in most cars, the primary means of limiting the amount of air entering the engine is a throttle valve which forces the engine to draw a partial vacuum; all energy spent drawing this vacuum is wasted; (2) no production engine that I know of has any speed-independent means of harnessing any energy left in the fuel/air mixture at the end of the power stroke; if the intake is near atmospheric pressure, and the expansion/compression ratios are nearly equal, the exhaust pressure must be significant for the engine to produce any meaningful amount of power.
I've read a white paper on the subject of using late intake-valve closure to reduce compression ratio (without affecting TDC volume or expansion ratio), and another paper (written by a FReeper) on the subject of using switchable compounding to double the expansion ratio. Although I am aware of engine designs which use unequal compression and expansion ratios, I am not aware of any common production designs that make them equal when maximum power is needed and unequal when it's not. Since most engines spend most of their time producing well under maximum power, allowing efficiency optimization for that case while also allowing power optimization when power is needed would seem like a major win.
"....harnessing any energy left in the fuel/air mixture at the end of the power stroke...."
there (above) is the pipe dream......the "smidge" of 02 remaining in the (pre-catalyst) exhaust gas is witness to (in a word) stoichiometric efficiency.
making use of the (catalytic) heat generated by what are literally trace amounts of HC and CO in the exhaust of a contemporary engine with all systems operating properly would be to add cost to a system/technology that long ago passed the point of diminishing returns.
your other concern, compression----remember, it works both ways on the piston equally with no fuel/ignition......and that low manifold pressure w/low throttle sense shuts off fuel these days (when "backing off" throttle/coasting).
P.S. - there is no cold, but there IS atmospheric pressure - I trust you git the drift :)
"....all energy spent drawing this vacuum is wasted....)
"gulp valves" (25 or so yrs ago) attempted to address this theory......they were quickly discontinued because they were so problematic driveability-wise, not to mention engine damage (from lean mixtures). An air inlet tee'd into the induction south of the carburetor.