What you are observing is called gauge pressure. Its common in things like tires or other pressure systems, where the gauge measures how far above or below atmospheric pressure something is.
It does that because the way gauges measure pressure is by having the gas in the container push against the surroundings of the gauge (usually on a spring).
So it just tells you what the pressure is vs the surroundings, where that is air, water, air on top of a mountain or whatever.
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