Hello Timtom,
Those factors are not being counted at all. Why? The software only knows about the two features (the two points you are getting the distance, the sphere/spheroid and a datum/projection factor).
For that to happen you need to probably use a developed linestring, in which you will connect your point with n vertices, each of them being Z aware.
Imagine this (loose WKT): LINESTRING((0,1,2),(0,2,3),(0,3,4),(0,10,15),(0,11,-1)).
Asking the software to calculate the distance between each vertex and summing it up, will consider the variations of terrain. But without something like that, it is impossible to map for irregularities in terrain.
All GIS softwares cannot tell, by themselves, what are those irregularities in terrain, and therefore, not take them in account.
You can create such linestrings (automatically) with softwares like ArcGIS (and others), using a line (between two points), and a surface file, such as the ones provided freely by NASA (SRTM project). These files come in a raster format, and each pixel has a X Y and Z value, in meters. Traversing the line you want, coupled with that terrain profile, you can achieve the calculation you want to achieve. If you need to have super extra precise calculations, you need a precise surface, and precise Z values in each vertex of this profile line.
That cleared up?