Correct it's resistance to air going in, so it's half the picture. Whereas VE is the efficiency of the engine to accept the available mixture into it's cylinders and exhaust them.
So with a normally aspirated engine at atmospheric pressure before the air filter the engine sees less after it. The airfilter lowers the manifold pressure.
Now in a turbo charged engine the waste gate is set to ensure the engine sees it's rated manifold pressure. So even if there was any impedance between the output of the supercharger and the inlet manifold the waste gate would counter this and ensure the rated pressure in the manifold.
And this is why it should be set to zero on a turbocharged engine in jsbsim.