A duplicate is a duplicate regardless of age.
It's true - more frequently newer questions are flagged as dupes of older questions, but in this case it wasn't appropriate.
The dupe question for yours is a canonical QA as to why one-click installer stacks (WAMP, XAMPP, etc.) are inappropriate in a professional sysadmin setting. HopelessN00b found your old question and marked it as a dupe of our newer, canonical question on this subject.
You will notice that he didn't just outright close your question - he locked it. The question is indeed off-topic, so closing would have been appropriate, but he (somehow) was able to find a bit of grace in his (two-sizes-too-small) heart and just lock/dupe your question instead.
To answer your explicit questions in a straightforward manner:
Why would this be considered a duplicate,
Even though it's not exactly a dupe, for instances like this where 1) the question is borderlin off-topic and 2) we have a canonical QA that covers the topic, we use the duplicate flag as a manner to refer people to the canonical answer instead of just closing the question.
and why would SF allow this kind of flagging?
Because any mechanism that can help organize and clean up things on the site are helpful. Why should they not allow this kind of flagging?