TD,
Usually an aircraft at "3,000" heading towards a runway at 1,234 ft above sea level, as possibly reported in broad terms in newspapers, would normally be in the approach phase of the flight. The pilot, in most places in the world, would have his altimeter adjusted such that would it read 1,234 ft on touchdown at that airfield.
So, yes, you're right. The aircraft would be in atmospheric pressure at sea level minus the pressure associated with the reported height. If you're interested in cabin pressurization, the aircraft at that phase of flight would be set to depressurize upon landing at the airfield, so the pressure difference on the approach is not related to the height above sea level but the height above the ground.
Hope this helps