By the way, I noticed that you still can't manually close a task.
Here is an example that happened to me: I pushed a commit to my work branch, and it caused an autoclose to the ticket (my bad as autoclose was not configured correctly). My final commit was pushed to master but I could no longer trigger the "Closed this task as Resolved by commit ...". Now it's just there stuck with the old commit. Removing the commit from the task did not help.

In T9232#133173, @chad wrote:

It's available on the commit under "Edit Maniphest Tasks".