This way we can point to specific areas of the FAQ to clarify my reasoning for flagging off topic.
If your intent to make clear about reason why you're flagging/voting to close and ensure that the OP sees why you're voting to close, then it's best to leave a comment. Your flag message contents are confidential and visible only to Mods. Once you've left a comment, go by the usual, Flag -> It doesn't Belong here -> Off-topic route.
Otherwise, as mentioned the other route is flag -> it needs ♦ moderator attention -> other -> enter your comment - but in this case, you're telling this only to the Mod who's acting on this ( and other Mods who might investigate the question) instead of guiding the OP as to why he shouldn't be asking such a question