It has previously been discussed in the infamous "Timelord" thread here, cross universe posts are only valid if there is a reason to suspect they are in the same universe. A specific example was mentioned of crossing Twilight Werewolfs with Harry Potter Werewolfs, they don't have anything in common, there is no reason to suspect they do, and should just be banned.
As to the specific question mentioned, there is absolutely no reason to suspect that a Harry Potter Merlin has anything to do with the Merlin from the myth. You yourself in your answer came to that same conclusion, although it was somewhat elegantly put. Merlin has a hundred different stories, and one cannot suspect that all of them are connected together. In the case where a character commonly used in mythology is adopted by a specific universe in a way that is different, it makes no sense to directly compare that character to the entire history of the subject.
However, there is some good material in this question. I've decided to edit it, and re-open it, based off of a more realistic question. See the question for my edit.