Normally in statistical mechanics and thermodynamics we assume the center of mass position of the system is at rest, since an overall average motion of the entire system is usually a distraction from studying the internal properties of the system. So this kind of position is not really part of the macrostate since it doesn't change.
In the context of Lagrangian fluid mechanics, you can consider a fluid element which is "small" compared to the entire volume of fluid but "large" in the sense that it is made of many particles, and ask how the position of this fluid element evolves with time. Since the position of the fluid element is an average of many particles, and therefore subject to statistical fluctuations, it is a macroscopic variable. I'm not sure, however, if it's useful to think of the position of a fluid element as part of the "macrostate" of a thermodynamic ensemble; my guess would be no... since you rarely are directly measuring the positions of individual fluid elements, and since in an incompressible flow there is no heat transfer at all. (However this isn't my area of expertise).
In the example given in your question, you are talking about the position of one microscopic doping site in a single microscopic unit cell of a crystal. I would consider the position of the dopant to be part of the microstate, and typically not something that is macroscopically observable. A macroscopic variable might be more like the fraction of all doping sites in the crystal that contain a dopant.