The only time the engine sees less pressure than atmospheric is when it's normally aspirated, and at part throttle. Boost is pressure above atmospheric, so if your "boost" guage registers anything above zero, it's added to atmospheric pressure. By adding 1 BAR [14.7 PSI] of boost, you're running 1 BAR of boost, but that is equal to doubling atmospheric pressure. For the sake of simplicity, you don't refer to the absolute pressure the engine is seeing though, that's why when your turbo is running 14.7psi, then all you refer to is the boost pressure, and not try to add in atmospheric pressure in with that boost reference, since atmospheric is a constant anyway.

Even when you measure your tire pressure, you aren't measuring the absolute pressure inside the tire, you're measuring the pressure above atmospheric. The reason being is that when your tire is inflated to 35psi, the absolute pressure inside the tire is actually 49.7psi, but there's also 14.7psi on the outside of the tire due to atmosphere pushing back on the tire.

The only time you need to worry about absolute pressure as opposed to differential pressure, is when you're dealing with different atmospheres. Last time I checked, the only careers that did that deal with NASA, and deep sea exploration.