VE actually has nothing to do with the exhaust system at all, at least, not directly. VE, the scientific definition, is purely cylinder fill relative to atmospheric density. 100% VE simply means that you have exactly the same density (at BDC) in the cylinder, as you do outside. There's really no consideration for intakes and exhausts in the calculation. However, both those items have an effect on VE. Ram air to tail pipe, soup to nuts, it all plays a role. But VE is simply: BDC Density/Atmospheric Density. And it's always calculated at full throttle.
Typical Naturally Aspirated engines in the 60's might have had a VE of 60%. Some as low as maybe 40, or up to 80. Modern hi-po engines, with variable cam timing, duration, etc can actually achieve a VE of 100%, or even over 100% in some of Honda's really hot applications. Yes, you can achieve a VE over 100% without forced induction. That gets into some crazy concepts that I'll leave out.
As I said, it's as simple as "BDC Density/Atmospheric Density". But intake and exhaust play a role. The intake has a very direct and obvious effect on VE. The exhaust also plays a role, because if the exhaust can't clear the combustion chamber to make room for oxygen, VE suffers.
Now, when cruising, most vehicles require something on the order of 20 hp. Not 200, or whatever the full power is. If you had a 100% VE engine that produced 200hp, you would require 10% VE to produce 20hp, assuming no frictional or thermal losses. Let's also assume it requires 10% throttle to let 10% air density into the intake manifold which results in the 10% VE. This is grossly over simplified, obviously.
Ok, so now we install a restrictive intake system, or a backwards snorkel or whatnot. This immediately reduces the full load VE from 100%, to 95%. At a 10% thottle setting, you might see more like 9.5% density in the manifold, producting 9.5% VE, and actually only making 19hp. So, the truck starts slowing down. What does the driver do? He opens up the throttle a little more. So, you open it to 10.5%. The extra throttle angle now allows 10% air density into the manifold again, which again produces 20hp.
So, to cruise down the road using 20hp, the engine has 10% air density in the manifold whether it is operating at 100% VE (measured at full load, VE doesn't get measured when throttled), or whether you have restricted it to 95%. That 10% air density requires the same amount of fuel to burn at stoichiometric ratios, and the same fuel economy results.
Obviously, the big things I've left out are: Engines have friction, and thermal losses. This is seen as an "energy overhead" which needs to be overcome. It is constant at a given speed and load. It might mean you actually need 30% air density in the manifold to achieve 10% power at the wheels. All of this is transparent to the previous discussion.
The other thing left out, is what I mentioned in my previous post. The computer looks at the throttle position to determine load demand. There is a cross-over point when the computer will switch from 14.7:1 Air/Fuel Ratio for emissions, to a "high power" AFR of about 13:1. It richens up the mixture to make more power from a given air density in the manifold. So fuel economy suffers. That is how a restrictive intake can affect a fuel injected vehicle.
One thing you may be interested in is the concept of "Load". Which is the instantaneous cylinder fill of an engine. At full throttle, VE is necessarily equal to the VE of the engine. At lower throttle settings, Load is closer to the air density in the intake manifold.
Again, to travel down the road at a given speed, you require a certain HP, which means a certain load on the engine. When you restrict the intake, you must open the throttle a little more to achieve the same load. This has no effect on fuel consumption, unless you cross-over into the high-power setting of the fuel injection system. The worse you restrict the intake, the higher throttle setting required, and thus the more likely you are to cross into the open loop setting of the ECU.
This can be a little hard to grasp, and I've seen many "professional" aftermarket engine tuners who don't really get this stuff. Once you start working with an elegant fuel injection system (I've tuned Pectel, and Ford's EEC IV) it's much more obvious what's going on.