All right, I understand the first and the third explanations, but I can't understand the second one. I'm sorry. So, could you please walk me through that?
As for these sentences that you gave me as examples:
- John will be calling in an hour, because he has a question.
- John likes that restaurant the most, because it has the best wine.
I can only see the because-clause as the main point of the sentence, and answer "why" John will be calling or "why" he likes that restaurant the most.
The comma before "because" is not necessary in those sentences. Indeed, if you were the writer and you did, as you say, understand the "because"-clause as the main point, then it would not make sense to use a comma there.
With those two examples, I was creating sentences that someone might use both to inform someone of something for the first time and to inform them of the reason for that thing. What follows "because" could be a separate sentence.
If you see the "because"-clause as the main point, then you are likely presupposing that the hearer/reader already knows that John will be calling in an hour or that John likes that restaurant the most. That need not be the case.