Before entering into the details an annotation. Normally in grammar books the reported speech and the sequence of tenses are considered two different phenomena that have nothing to do with each other. That's wrong. The reported speech is only a special case of the sequence of tenses in general. Let's start from the beginning.
If we tell something that someone else told before we use the reported speech.
direct speech => Maria: I am hungry
reported speech => Maria says that she is hungry.
In this ficticious situation a second person, a ficticious Roberto for instance, tells us what Maria has told before. Before we explain the central problem of the reported speech and the sequence of tenses let's see what is the sequence of tenses. The sequence of tenses is very similar to the reported speach. In the sequence of tenses the events / actions of the subordinate clause are described as something imagined because someone thinks, fears, hopes, dreams, believes that something happens, happende or will happen.
directly => Maria: I think, he is ill.
reported => She thinks, that he is ill
We can see that the difference is not so big. In this case, our fictitious Roberto tells what Maria is thinking. What is the central problem of this kind of construction? The central problem is that in both constructions we have to respect the chronological order, in other words it must be clear whether the actions / events of the subordinate clause (had) happened before they were told / imagined, are happening at the moment they were imagined or would / will happen after they were imagined. In both cases the introductory verb which describes the type of imagination (believe, fear, etc.) or the way the events / actions are told (tell, say, inform, etc.) can be in the past or in the present and in both cases it must be clear if the event / actions happened before, at the same time or after they had been imagined. The anchor on the timeline is the introductory verb which describes the mental penetration.
sequence of tenses: Verb is in the past
before: I thought that he had come
at the same time: I thought that he was coming.
after: I thought that he would come.
sequence of tenses: Verb in the present
before: I think that he has come.
at the same time: I think that he is coming.
after: I think he will come.
reported speech: Verb in the past
before: She said that he had come
at the same time: She said that he was coming.
after: She said that he would come.
sequence of tenses: Verb in the present
before: She says that he has come.
at the same time: She says that he is coming.
after: She says he will come.
It is crucial to understand that in both cases the anchor on the timeline is the moment where something is imagined or told and NOT the moment where someone else tells or imagines what someone else has thought or imagined. Let's see an example. On Monday John breaks his leg. On Wednesday Maria thinks / tells that John broke his leg and on Friday Ricardo thinks / tells what Maria thought or imagined.
Ricardo on Friday (Two days later, Maria thought it on Wednesday)
She thought / said that John had broken his leg.
In this case we have to use the past perfect because the anchor on the timeline is Wednesday and not Friday. We have to use the past perfect because we have to describe an event / action (the breaking of John's leg) which had happened, from the perspective of Ricardo, before another event in the past (the thought of Maria).
We see more clearly that the anchor on the timeline is the moment where something is imagined / told when we change the example a little bit. Let's say that John does something risky on Wednesday and Maria fears on Monday (two days before) that John will break his leg on Wednesday and Ricardo tells on Friday what Maria feared on Monday.
Ricardo on Friday:
She thought / feared that John would break his leg.
In this case it is more obvious because we use the conditional I, which describes in this context an action in the future from a point of view in the past (Monday => Wednesday). In other words, from the perspective of Maria something that is going to happen on Wednesday is in the future. From the perspective of Ricardo the risk to break a leg is in the past, but his point of view is irrelevant in this context.
We have seen until now two things. Concerning the central problem, the alignment of the actions / events on the timeline there is no difference between the reported speech and the sequence of tenses. The reported speech is only a special case of the sequence of tenses and therefore it doesn't make any sense to treat these two things in different chapters. The anchor on the timeline for the events / actions described in the subordinate clause are the moment where these actions / events are imagined / told and not the moment where someone else imagines / tells what the other imagined / told.
That's the reason we treat the sequence of tenses and the reported speech in the same chapter. In the following chapters we are going to discuss that in detail.