Comment 2 for bug 1274342

It is a known issue, and it was not an oversight. See:

    http://askubuntu.com/questions/382703/faac-in-ubuntu-13-10-doesnt-support-mp4

It was removed due to licensing issues -

faac (1.28-5) unstable; urgency=low

  [ Andres Mejia ]
  * Disable mp4v2 support.
    This only disables mp4v2 for the faac utility program. The faac
    utility is GPL-2 but the mp4v2 library is MPL-1.1. The two licenses
    are incompatible with each other.

  [ Reinhard Tartler ]
  * Revise debian/copyright
  * Bump standards version (no changes needed)

 -- Reinhard Tartler <email address hidden> Sat, 22 Jun 2013 15:09:31 +0200

Which means that Debian and Ubuntu cannot distributed faac with mp4v2 support until this licensing issue is resolved.
In the mean time, it is probably the easiest to rebuild faac ourselves with libmp4v2-dev installed.