Each z-level can be thought of as layerd but separate dimensions, with each plane only interacting with the others near it in three different, limited ways: stairs, ramps, and the dimensional displacement phenomenon hereafter referred to as the Feb Effect that occurs when objects in projectile motion occasionally have a component of velocity in the z-direction. Individual creatures have only partial perception of these phenomena, being capable of perceiving, in a limited sense, the immediate area surrounding a ramp or stair. They are also able to aim projectiles at targets on other nearby z-dimensions through estimation based on distortion in the empty floor and ceiling space, but with increasing difficulty as the dimensions grow more and more distant and visual artifacts grow more faint.
Siege weapons are, technically speaking, constructions. This means that they, like others, only have presence on a single z-level. Their inherent two dimensional nature makes it impossible for them to be adjusted to take advantage of the Feb Effect. To compensate for this, Dwarven engineers give the siege engine tremendous mechanical power. This both allows them to fire much farther than the average operator can actually see and, in the case of catapults, actually gives the projectile sufficient energy to bend space around it. It is theorized that this is the result of a fractional bending of dimensional space, such that the catapult shot moves beyond it's original z-dimension, but does not quite reach the one "above" it. A side effect of this phenomenon can be observed in the massive loss of velocity, and therefore killing power, of the catapulted projectile upon reaching it's target.
Why do siege engines only require three of a generic [engine] part to build?