The meta discussion says that to close a question with a bounty, you should raise a flag. I did that. The flag was declined. This question is not about why it was declined, but rather about the moderator's statement that "You can vote to close if you like." How?
Moderators can unilaterally close bountied questions, and refund the bounty, as explained in the linked meta question. However, I would use such a heavy intervention only for blatantly off-topic questions or egregiously problematic ones. I don't see, at the moment, any such case.
For all other questions, I suggest to let the bounty follow its cycle and then vote to close, so that other regular users can vote on it.