<p><a href="http://meta.stackexchange.com/a/185873/189912">According to Shog9</a>:</p>

<blockquote>
  <p>That was a last-minute bug fix. See, while meta let you enter a custom reason, it didn't actually <em>do</em> 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.</p>
  
  <p>Folks who can vote to close directly still have the option, and it creates a comment along with their vote.</p>
  
  <p>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.</p>
  
  <p>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. </p>
</blockquote>