For some reason I only just now noticed that I can choose to either flag a question for moderation, or opt to close it.
Is the second option really just a shortcut (of one mouse-click less) to that particular subcategory of the 'flag' option, or is there more to it?
If you have 3000 reputation, there is no difference when you flag to close something. It just uses your close vote.
Flagging is more for the areas where you don't have the privileges to enact something, but to bring it to the attention of those who do. So flagging to close something dumps it into the Close Vote queue for others to take a look at, same as using your close vote, it just doesn't have a close vote from the flagger.