This talk (not from a Goenka perspective) really helped to clarify the issue for me.
Thanissaro:
...as you're learning to comprehend suffering, there should come a point when the mind realizes: This is not worth it. The image the Buddha gives is of a blind man who has been given a soiled oily rag. The person giving it to him tells him that it's a clean white rag, so the blind man is very protective of it. He folds it up, and takes very good care of it because he thinks it's a nice white piece of cloth. Later, when he's finally he is treated by a doctor and gets his eyesight back, he can see what it really is: It's just a soiled old rag.
So this is why we try to comprehend the five aggregates, the six sense media in terms of those three perceptions: to see that they're just soiled old rags. At the same time, we're looking for where the gratification is in holding onto them — our ignorant misunderstanding that they're something of value. Then you want to comprehend the drawbacks of craving these things until you really do develop a sense of dispassion. With the dispassion, you start letting go of the craving.
[Further on...]
All these teachings have their strategic purpose. And it's important that we keep using them for their strategic purpose. We're not here to argue, we are not here to establish the one right view about reality. We're here to find ways of putting an end to suffering.
So remember those three perceptions. And that's what the Buddha called them, "perceptions": the perception of inconstancy, the perception of stress, the perception of not-self. He never called them characteristics. He never talked about three characteristics. You do a search for the term, "three characteristics" in the Pali Canon, and you're not going to find it. The Buddha's talking about a way of perceiving that helps you see through your attachments, that helps you see through your delusions about where you can find happiness, so that the question that lies at the beginning of wisdom — What when I do it will lead to my true long-term welfare and happiness?" — finally gets its answer in the skills you've developed.
([url=http://dhammatalks.org/Archive/090420%20A%20Soiled,%20Oily%20Rag%20(3%20Perceptions%20in%20Context).mp3]audio of talk)