The units still base the elevation from the WGS84 ellipsoid. Different units do this differently.
For aircraft, the altitude is still based from the WGS84 ellipsoid, and again, depending on the box, calc it differently. Smiths uses a grid over the ellipsoid with a lookup function. Honeywell interprets the ellipsoid.
Because the shape of the Earth is not symmetrical, the ellipsoid is an approximation, and the altitude generated by the box, needs to be further corrected.
That is why, when you look at the diagram of the ASBL, it looks so odd.