According to the rules book, the 3rd column of favours is available after the scoring of the dungeon. My question is, when scoring the dungeon, is it still considered as before the scoring? In other words I can't move my marker up to the 3rd row to collect 3 points or build a stone building, with the favours I've earned right after scoring the dungeon, correct?
Right: you can't move my marker up to the 3rd row to collect 3 points or build a stone building, with the favors I've earned right after scoring the dungeon. See the example on the last page of the rules:
Orange has just gained a favor during the Dungeon scoring. He chooses the first line (prestige points), on which he already advanced in a previous phase. However, since the Dungeon is being scored, Orange can’t advance his marker. He leaves it on its space and gains 2 prestige points.