No. The only reason that you are confused is because you are trying to make 'rules' when there are none.
Try to accept that that all conditional sentences are in a way hypohetical. The possibility of the realisation of the hypothetical situation ranges from effectively 100% ( the so-called 'zero conditional') to effectively 0% (what some of us call counter-factual). Context, co-text and the shared knowledge of speaker and listener usually make the intended meaning clear. If it does not, questions may be asked and/or further information given:
A: John arrived an hour ago
B: Well, if he arrived an hour ago, we must set off now.
C: If he had arrived an hour ago, he would be here ago.
A. He arrived! he called me half an hour ago.
B is almost certainly indicating acceptance of the factuality of A's first statement. However, intonation, particularly a heavily stressed 'if,' would suggest doubt about this. We cannot say absolutely..
C is almost cartainly indicating strong doubt, perhaps even disbelief about the arrival.