Is it the case that the plot must be labeled with particular units, or is it the case that the plot must render on the screen a particular physical size because you need people to be able to literally put a ruler to the screen to measure distances? And is the question how to make the Z axis measurable by placing a ruler on the screen?
If the question is how to make Z measurable on the screen, then you need to choose your viewing angle and projection matrix very carefully, and the user has to do some interpretation to figure out which of the infinite number of x, y, z coordinates that project to the same screen x y point is being referred to.
But if the point is to make that kind of measurement, then why not just let the user click on the points and have the computer tell the result?
