[According to Shog9][1]:

> That was a last-minute bug fix. See, while meta let you enter a custom reason, it didn't actually *do* anything with that reason. This isn't ideal. So it was fixed before the network-wide rollout, and should disappear from Meta as well soon.
>
>Folks who can vote to close directly still have the option, and it creates a comment along with their vote.
>
>We'll revisit the need for a low-rep user "other" option based on usage, but initially we're trying to restrict the use of flag-to-close to problems that are generally agreed-on by the community.
>
>If you see a post that should be closed for an unusual reason, you have the option of flagging for moderator attention, selecting "other" and describing that reason in detail. 



  [1]: http://meta.stackoverflow.com/a/185873/189912