Hi Siebe,
The bodily pain arising due to the ripening of a kamma vipaka is not the dukka sacca the Buddha talks about. The Buddha eliminated all future suffering when he attained enlightenment. This means that he will not experience any dukka in this life time too. However he did experience kamma vipaka, which brought him bodily pain. So we can see that the bodily pain brought about by a ripening kamma vipaka is not the dukka he was referring to, when he said he eliminated all future dukka.
You said “sometimes there seems to be no real reason to be irritated or heated up”. Yes, I think we have all experienced something like this. But if we really sit back and look for the reason, it will turn out to be because of anicca. Most often the reason we don’t understand this is because we are too engrossed in this irritated state of mind, we are blinded by it that we can’t think properly. Either way I don’t think that an arahanth, someone who has completely eliminated future suffering, would get irritated and heated up like normal people do.