Let's stick to VE for now, please
What's the explanation, then? Why would increasing the pressure of the air coming into the cylinders modify the relative volume occupied by that air in the cylinders?
Starting from the ideal gas law: n = p * V / R * T . Compressing the air that comes into the engine modifies the 'p' term, thus increasing the air quantity, but it can't modify the maximum volume that the air can occupy compared to the NA route.
Starting from your example, having a 1bar boost pressure and let's assume a 1000cc engine.
NA:
p = 1 bar
Veng = 1000cc
Vair = VE * Veng = 1000cc
NA: air quant = p * Vair / R * T = 1000 / R * T
Turbo:
p = 2 bar
Veng = 1000cc
Vair = VE * Veng = 2 * 1000cc = 2000 cc
Turbo: air quant = p * Vair / R * T = 4000 / R * T
As you can see, increasing the VE and still accounting for air pressure translates a doubling of the air pressure into aquadrupling of the air quantity, which is simply not correct.