Havent seen binaries for MacOSX that understand H.264.
Just do
mp4creator -l bla.mp4
this will show you the tracks,
and then something like
mp4creator -hint=1 bla.mp4
and
mp4creator -hint=2 bla.mp4
It is fast, but a script will not be easy to write, not all movies are
the same.
But it is much faster than QT pro!
If you need to add hint tracks through scripting to automate the
process, the mp4creator tool from the MPEG4IP
(http://mpeg4ip.sourceforge.net/) package might be what you're looking
for.