QWhen an ability refers to the cost of a card that was played for a different number of play points than its displayed cost, does it refer to that different number?

ANo. It refers to the cost displayed on the card. For example, when referring to the cost of a Flame Destroyer, the number used is always 9, even if it was played for 6, 3, or 0 play points.

Effects that change the number of play points it costs to play a card don't change the cost information of the card. When an ability refers to how much a card "costs" or its "base cost," it always refers to the cost displayed on the card. Note that, when referring to the cost of an evolved follower, you use the cost of its unevolved form.