The Help Center page Cast Close And Reopen Votes contains some text which (probably because of changes in the flagging system) is a little bit misleading:
Note that once you gain the reputation to vote to close, you should no longer flag for moderator attention to have questions closed or migrated.
You should never flag for moderator attention to have questions closed (the sole exception being a question with an active bounty), and flagging for migration is still a valid option if the target site is not among the predefined migration targets.