As I can see it, "Miles thought"- is the past time. The events in its thought take place much earlier than the moment of the thought. So, why the man in Miles' thought "said", but not "had said". Doesn't using the words "said" and "thought" mean referring to the same period of time? The same thing for "He sent the young man"..."A young man named Hugo came to the inn and said: 'Tell the boy to meet Miles Hendon at Southwark Bridge', and the boy went away." "That man!" Miles thought. "That man who said that the boy is his son! He sent the young man!"
But the most confusing thing is why the boy "is his son"... It sounds like that is some generally accepted and known to the world fact, that that boy is a son of "that man".
I would rewrite the last sentence from the quote above as follows:
"That man who had said that the boy been his son! He (had)sent the young man!"
What would you say about it?