You have that backwards - higher number is LESS vacuum (i.e. higher pressure)
The cylinder pulling 540 has BETTER vacuum (lower pressure) than the other two.
Why are they different?
Because the balance screws adjust the relative 'closed' position of the throttles (they are not really closed - if they were, there would be no airflow at all and the engine would stall)
The one with 540 has the throttle 'more closed' than the other two. (or conversely the other two are 'more open')
At sea level pressure is ~ 1013 hPa (or mbar) - if you go to say 5000' (colorado for example) then atm pressure is ~ 840 hPa
At 10,000', atm pressure is ~700 hPa
Altitude above Sea Level and Air Pressure
At idle, the throttles are closed, therefor it creates a low pressure in the throttle bodies as the pistons pull against them;
when you open the throttle, it lets air in so the pressure will try to normalize to that above the throttle.
The highest vacuum, (lowest number) will be if you rev the engine then close the throttles - this creates a higher excavation rate of air from the area below the throttles, therefor the pressure drops.