What is required here is the Third Conditional, in which the speaker imagines a situation which hasn’t actually happened. In this example, the speaker didn’t know the person addressed was coming, and so, we are led to believe, the speaker came as well. The usual form taken by the Third Conditional is if + past tense of have + past participle of the main verb, followed in the main clause by would have + the past participle of the second main verb. This produces If I had known you were coming, I wouldn't have come. A simpler example is If you had run, you would have caught the train.
The past tense may sometimes occur in the if clause (If I knew you were coming . . .), but in British English, at least, it would be unusual. That said, I expect some of us will know the song that has the line If I knew you were coming, I’d have baked a cake.
I don't think your idea can exist.
In your sentence...
I can have had been reading a book if I could send a letter back in time to tell myself.
... the conditional if and past-tense makes your opening can illogical.
Instead,
I could have been reading a book if I could have sent a letter back in time to tell myself to read it.
-or-
I could have read a book if I could have sent a letter back in time to tell myself to read it.
-or-
I could be reading a book if I could have sent a letter back in time to tell myself to be reading it.
If you're writing fiction, and the idea you're trying to communicate is that you could be doing something else right now if you could change the timeline, I would say it like this:
If I can send this letter back in time to myself, then I can have read the book before it's too late.
When you try to say "I can have had been" you're creating a time paradox. Consider the following:
I can be reading if I can send myself a letter back in time to tell me to be reading.
If the above is true, why aren't you reading? And if you were reading, you couldn't be sending yourself a letter to tell yourself to read, so you wouldn't be reading.
So, like I said, I don't think the idea (as you've expressed it) is able to exist, the grammatical problem merely uncovers the time paradox.
Best Answer
In short: no, this usage of would have been is correct, and its meaning is subtly different from would be and were here. It is probably useful to look at this sentence one step at a time, to consider each transformation of the verb separately.
A simple statement about a present fact. (The default attitude of a speaker towards a proposition is "this is true", so fairly strong certainty.)
The verb is transferred to the past: a simple statement of fact about the past.
In this transformation, have been is equivalent to were as above; will is added to express "I expect that this will turn out to be true". It calls some attention to the (confident) attitude of the speaker towards this "fact of the past"; one could say that the speaker shows that he is aware that he is giving an estimation, not a completely indisputable fact. But instead of may, he uses will to express that he is quite confident about it.
I do not think this is habitual will/would, because to describe a repeated situation in the past you would simply say they would be alone when travelling. You could do that, and the meaning of the sentence would not change very much, because the speaker's attitude is not that important to the meaning of the whole sentence; but it would still be slightly different.
The condition when travelling makes it a habitual/repeated situation anyway: they were not alone when travelling would express that they were not alone "every time they travelled". So the habitual nature is probably not contained in will/would.
Here will changes into past subjunctive would. This could be considered a conditional would, as in "if I should be right, they would not have been alone", or some other condition. As an alternative, you could simply say that the past subjunctive can be used with modal verbs to add more uncertainty in general.
I do not think there is a clear boundary between the two. The more general uncertainty as perceived in would where no clear condition is present (explicitly or otherwise) probably originates in that very conditional construction: a condition adds some degree of uncertainty to any proposition, as it will only be true under certain conditions. You could call would "epistemic" when no condition can be easily conceived of, but it is really immaterial.