You're right about the application of the present perfect, but you've not noticed that because of the "present relevance", it is incompatible with an expression of time that doesn't include the present.
"I have marked those books today"
is fine, and so is
"I have marked those books this morning"
if it is still morning. But if it is now afternoon, then the latter will not work, and
"*I have marked those books yesterday"
is never acceptable.
Your characterisation of the past perfect is incomplete: it is not enough tha it have relevance in the past, but requires that there be a particular point in the past, which has already been established or is otherwise obvious to the participants in the conversation, at which the action had relevance.
"I had marked those books"
is acceptable provided the previous conversation or something about the context has established the point in the past about which you are talking (not the time when you marked the books, but the time at which you could have said "I have marked those books"). Using the past perfect when there is no such point of time in view is strange.
Generally, expressions of time which do not include the reference point are similarly not acceptable; but there can be exceptions. If you and I talked yesterday about some books, and I had been unable to remember when we talked whether or not I had marked them, then I might say
"I had marked those books yesterday"
where "yesterday" serves to identify the reference point, and means "when we talked about them yesterday". It would not necessarily mean that I marked them yesterday, as opposed to on a previous day.