I wonder when this flag "it should be closed for another reason…" should be used. Is it not the same flag as it "needs moderator attention"?
The "it should be closed for another reason…" flag is the flag that should be used to close a question that is not duplicating another question. In fact, the previous flag is "it is a duplicate…."
It is different from the "other (needs ♦ moderator attention)" flag, since the first adds the question to the Close Votes review queue, accessible to all the users who can vote to close; the other flag shows up the question in a queue visible only to moderators, as only moderators see those flags for which the user entered a custom reason.
That is the reason why a custom reason should be used only for specific cases that really need moderation attention.
Keep in mind that flags that are not for closing a question have as last destinatary the moderators, even though they are visible to other users as well (with the exception I reported before). You should not flag something that doesn't really need attention from moderators. (I know you already know this; the note is for future readers.)