Mike - if the reflector is a true parabolic reflector, the light from the reflector should be hitting the water surface at 90 degrees to the surface, No matter what the height of the reflector. So, for the reflected light, height makes no difference.
For the direct light, as the angle between the light source and the water surface decreases below 90 degrees, the amount of "lost" light (light that is reflected rather than enteringthe water surface) increases. So, the closer the bulb is to the water surface, less the area of tank that is illuminated by light penetrating the water.
For simplification purposes, lets assume that very little light penetrates when the angle is less than 45 degrees. So, only half the light coming from the front (bottom) side of the bulb does any good. The rest, even though it hits the water surface, is reflected away (this is a simplification, but the general idea holds) becausethe angle the light hits the water is too shallow. But, almost all of the light from the back (top) of the bulb hits the reflector and is reflected down at 90 degrees to the water surface. (note - therein lies the advantage of the DE bulbs - the bulb body itself blocks less of the reflected light than a SE bulb).
Therefore, most of the light actually enterring the tank comes from the reflector, and with a proper reflector, height above water has minimal effect.
Another consideration - With the bulb at 3" above the water (your previous example, Mike), you are only illuminating a 6x6 square by direct light. Raise the light an additional three inches, and you are illuminating a 12x12 square. Yes, the illumination on that 12x12 square from direct light is less intense than the light on the 6x6 square from direct light, but who wants to have 'spotlight" areas. Plus, there is still more light enterring the tank from the reflector.
Most reflectora are somewhat of a compromise between reflector size and area covered. A true parabolic reflector would only light (by reflected light) the area directly under the reflector. Most of the better reflectors allow for a slight amount of spread from the reflected light in order to illuminate a larger area without having to have such a large reflector. But they still keep the light at close to 90 degrees for maximum penetration.