In my earlier days, I built my own flow bench and engine dyno and spent many years doing professional cylinder head and engine development for road racing engines- mainly on Toyota and Nissan engines. I've done thousands of flow bench and dyno runs on several different dynos.
The flow bench is a very useful tool but gains there don't always translate to gains on the dyno which is always the real proof that you're going in the right direction.
I see lots of folks worried about flow at .025 or even .050 valve lift however the amount of flow down there is a small percentage of half or full lift valve flow which constitutes the bulk of the valve open time (duration). Low lifts contribute minimally to filling or scavenging the cylinder, especially it you look at how long the valve is open at these small lifts. Total flow is a product of flow and duration. Flow is highly affected by delta across the valve which changes with piston position. The piston moves slowly near TDC and BDC where intake and exhaust valves are open only small amounts. Delta is low, flow is therefore low.
I pulled this out of my flow bench archives to illustrate:
.050 valve lift intake flow 14
[email protected] 10 inches H2O
.600 valve lift intake flow 129.0
[email protected] 10 inches H2O
.050 valve lift exhaust flow 8
[email protected] 10 inches H2O
.600 valve lift exhaust flow 89
[email protected] inches H2O
Simple flow benches simulate steady state flow and X pressure differential but that's not what happens inside a running engine where volumes and pressure deltas have infinite changes.
VE describes how much air an engine can induct in relation to it's cylinder displacement and is always highest at torque peak rpm.
Since flow is so low at low lifts, this translates into slow flow and slow velocity changes within the intake and exhaust passages when you look at the volumes you are filling and emptying.
The impact of slightly less chamber volumes going from 10 to 12 to 1 CRs is very minimal in how rapidly the pressure deltas change with the piston near TDC and low valve lifts there. Therefore it's impact on cylinder filling rates, hence VEs, are minimal. The bulk of the inducted air is moved during the half/ full/ half valve open period where exposed valve aperture is large and pressure deltas are large. Charge inertial effects are huge at high rpms and you need big and rapid Delta P changes to affect the charge inertia. This isn't happening at small valve lifts near TDC.
Most VE increases come from optimizing "wet" flow in the head (fuel droplet size and movement important), camshaft design and intake/exhaust optimization. CR is determined usually more by the fuel octane which will be used in a particular engine and that may be one of the very first considerations when developing any new engine for stock or racing applications. In other words you pick CR first and that is fixed for the rest of the design decisions you make down the line. Not much you can do about it.