I agree with your logic; it doesn't make sense to close a question as a duplicate when the target is closed as "unclear what you are asking." That said...
This particular situation arose because a new user apparently wasn't familiar with the capability to edit his question. He was kind enough to provide more details in response to the petitions, but he didn't include that information in the original question. And now that both questions have answers of different types, things are a bit messy.
I can't really blame close voters here, because the newer question is clearly just a fleshed out version of the original question, and closing the newer question might encourage the user to edit the original one. Now that both have answers, though, we need to reevaluate.
The key difference between the two is that the newer question is actually answerable, whereas the original one wasn't. Thus, if anything were to be closed as a duplicate, it should have been the older question, not the newer one (there's no rule saying that the older question is never the duplicate; if the newer question is better in some way, or has better answers, it can take precedence).
Thus the best path forward seems to be to open the newer question containing more details, and either 1) leave the older one closed as unclear and leave a comment pointing to the newer question or 2) reopen it and then immediately close it as a duplicate of the newer question. I don't see much practical difference between these two options, except that option #1 is slightly less disruptive.
So I've done exactly what I've described. If someone else has a better solution, feel free to suggest it. And as lessons for the future, we can be sure to encourage new users to use the "edit" link to modify their posts, and we can encourage close voters to remember that sometimes it makes sense for older questions to be closed as duplicates of newer questions.