One example of this is here, but I have seen several.
If the questioner is asking B, presuming A, could a valid answer be that A is incorrect?
Yes, but only if the asker's presumption of A actually affects B. For example, suppose someone asked:
I know kidush l'vana (said each month in the first half of the month) cannot under any circumstances be said indoors. Suppose someone cannot get outdoors for medical reasons. Can he fulfill his obligation by listening to another through an open door and saying amen?
And someone answered:
You're incorrect that it cannot be said indoors. He can look out a window at the moon and say it that way.
That's not an answer. The question was whether the homebound person can fulfill his obligation by listening to another. This answer doesn't address that.
But suppose someone asked:
I know Yom Kipur has never been Friday. Why, then, does Source X, which is always practical, discuss what happened when Yom Kipur would be Friday?
And someone answered:
Actually, Yom Kipur was Friday in year Z, before we had our fixed calendar.
That'd be a great answer. It refutes the presumption in such a way that makes the question disappear.
Moreover, consider the question you link to in your question:
I understand you can't say Tehilim at night. Can you say Tehilim between shkiah and tzeits hakochavim (ben hashmashot)? or does it have to be said before shkiah?
Suppose someone answered:
You're incorrect that you can't say T'hilim at night. The question you link to only discusses learning T'hilim at night. I've found no one who holds you can't say T'hilim at night, and Sources A, B, and C say you can do so. Therefore, you can certainly do so during ben hash'mashos.
That'd be a great answer. It not only refutes the presumption so the question disappears (as the Yom Kipur answer did): it even answers the question.
A specific case I assume we can all agree on in which it is not an answer:
Q: Commentary A says Y. How does this fit with Z?
A: Commentary B argues with commentary A.
In this case, the question is not on the assumption of Y. It is asked in the context of the fact that A says Y. There is no value in negating the given premise of the question.