I'd say option (b) too because it's important that it's in
undisturbed airflow. I'd only really consider the boundary layer with respect to the lifting characteristics of the wings (PoF).
Having said that, you are correct, the options are not that dissimilar. I wouldn't stick a pitot tube in the boundary layer either because, by definition, the airflow closer to the airframe will be slower that in the freestream. I guess in practice, the boundary layer is quite shallow and so it can be ignored to an extent?
Typical JAR ambiguity it seems...
Good luck with the rest.
0918