I'm not suggesting the Pioneer and Fly-By anomalies are related, nor am I suggesting the paper in question explains either of them. The paper merely reports the data as accurately and as free from systematics as possible. They do make the point strongly though that there is a component of the measured acceleration that is not explained by the theory of Newtonian N-body gravitational interactions.
My point was that there are other anomalies that haven't been sufficiently explained that relate to 'in outer planet satellite trajectories', which you suggested were okay in your post.
We may be simply mis communicating with each other as it appears you are well aware of the pioneer anomaly.