Basically, these meanings don't work for me:
question: "Is it never possible?"
response: "It is." (meaning "It is never possible.")
I would interpret this as meaning that it is sometimes possible, etc.
if your question is
"Is it that he is not here?", the verb you are answering is the first, is, which is positive, so the answer, "yes, he is not here", is right. If the question is "Isn't he here?", then the answer is "No he is not". Actually the first question is a positive question with a negative object. HOpe this helps.