If he had come yesterday, I would have gone.
That possibility refers only to the past. So, no, had come cannot refer to the future. However, had come tomorrow" is completely grammatical. Please read on. You can put in any time word/period: tomorrow, yesterday, in two lifetimes, it does not change how the sentence works.
For a possibility that has yet not materialized (future) when I speak to someone in the present time I say:
If he were to come tomorrow, I would go.
That same idea: were to [verb] is expressed like this:
If he came tomorrow, I would go. [It is not likely that he will come]
And if the possibility is not as remote as in the previous two sentences,I would say:
If he comes tomorrow, I will go.
A less strong improbability than the two previous sentences. The possibility is less iffy than with "were to [verb] or the verb in the simple past.
EDIT to my original answer:
Please note what Rodney Huddleston says about this issue in his book The Verb in Contemporary English: Theory and Description doubly remote conditional
He gives the following examples: [page 110]
If they go tomorrow,they will meet her son. [open]
If they went tomorrow, they would meet her son. [remote]
If they had gone tomorrow, they would have met her son. [doubly remote]
These are the exact same examples in terms of verb tenses that I gave above (spontaneously). I just didn't name them formally. Traditional grammar calls these first, second and third conditional. A conditional by definition is an if- proposition or assumption. Therefore, it is not about the future.
These sentences can be spoken in the present time of speaking about an unmaterialized set of circumstances or they can be spoken in the present time of speaking about a past set of circumstances. However, in none of these, are they sentences "about the future".
Therefore, the sentence "If he had come tomorrow [or yesterday or next week or whenever], I would have gone" are all grammatical but the use of an adverb of time does not change the fact, none of them are future.
So, I repeat what I said at the beginning "had come" cannot refer to "the future". It only refers to an unmaterialized possibility uttered in a present time.
Indeed, imagine this situation: You (John) are in an office working with an assistant. Some visitor shows up without an appointment. You realize you have no time to meet with this unexpected visitor. You see the visitor through a glass partition window and you say to your assistant: "If he had come tomorrow, I would have met with him."
The implication here is? The guy showed up at your office. Please note the preterit: showed up. Only then does John (the person in the office with an assistant) say: If he had come tomorrow, I would have gone. [logic: But, the visitor didn't come the next day, he came on the day John uttered his sentence.]
What is the implicature (as grammarian says, which is also an implication)? It is that the entire idea of "had gone" revolves around a preterit and not the future. If you read the rest of the paragraph by Huddleston in the link, that will become very clear.
So,to answer the question: Does "If he had come tomorrow, I would have gone." convey: "He will not come and I cannot go." No, it does not convey that. It conveys in the present time of speaking a possibility that is unrealized.
This sentence by Mr. Huddleston: If they had gone tomorrow, they would have met her son. [doubly remote] is the same exact structure as: If he had come tomorrow, I would have gone. The word tomorrow could be: tomorrow, yesterday, next week, in another lifetimes and nothing would change that fact.
And using If + had gone [past perfect + past conditional [would have + past participle] in the second clause is exactly what 3rd conditional is in traditional grammar. They are horses of the same color with different names. Conclusion: Double remote conditional is Mr. Huddleston's name for what traditional grammars call third conditional as given in the book cited above by him. Naturally, all sorts of other possibilities abound.