Leaving both KCs out in the stacked situation is probably a more technically correct way to handle it, and is the way that Donald had originally made the ruling. As guided said, this method is just harder to do in practice, so it has been settled on just leaving out the KC or TR that directly effected the duration card. If you stacked them, and as such, played 3 Fishing Villages all off of the same KC, I would think it is simple enough to just stack all 4 cards.
As for your question, my interpretation of the rule would be that if you played 3 KCs separately on actions, they would all need to stay out because that is the representation of what happened on the previous turn. That just seems more correct. If the draw back of not getting to clean up your KC cards is purely a side effect of needing a rule to track how the durations were played then I suppose I can see it being okay to clean up two of the KCs and stack everything up as if you had played them all on their own. However, this thought process would extend to being able to stack 4 KCs, and triple 7 duration cards, and still only leave out one KC to mark all of them.
I think leaving things as they were played makes more sense, but as long as everyone is doing the same thing in your game, I don't think it matters.