To which reference point on the aircraft is the altimeter reading relative to? To which point of the aircraft is the altimeter reading referred to? Is it referred to the probe position or is it offset to read as if it was at the bottom of the fuselage or the landing gear? If it was a GA aircraft I suppose it wouldn't make a difference, but on something big as a 747 or an A380, should it be set at the same level as the probe, there would be quite a difference compared to the ground (maybe 20-30 feet?). If so, how is this handled?
The placement of a probe for a pressure  altimeter has exactly the problem you mention, but they only need to be accurate within 75 feet, so placement is not a problem. 

For large aircraft, they use a "radar altimeter" which uses an electromagnetic beam to measure the distance to the ground, the same way police radars measure car speed. Radar altimeters are accurate to within a couple of feet.