>latencies of the order of 10-100 ns unexpectedly added or subtracted to a baseline
Perhaps my stats is a bit rusty, but if its the discrepancy is +60ns (only plus) & <20ns uncertainty, doesn't that rule out a -+100ns source (plus minus) as the cause of the (possible) error? i.e. We should be looking for an issue that shifts the results, not something that is adding noise.
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.
Perhaps my stats is a bit rusty, but if its the discrepancy is +60ns (only plus) & <20ns uncertainty, doesn't that rule out a -+100ns source (plus minus) as the cause of the (possible) error? i.e. We should be looking for an issue that shifts the results, not something that is adding noise.