I think that the author's point is that these latencies would, in fact, add a systematic bias to the measurements (i.e. they would shift the results, not add noise). I interpreted "added or subtracted" to mean that this bias could either be added at the source end or subtracted at the receiving end.
The diagram being discussed is labeled "LNGS" so I'm pretty sure it both green and blue relates to one end (receiving), just different parts of the receiving end.
