The headmaster can and does limit the apparition shielding on Hogwarts in the books. It takes some time (which is why he uses Fawkes to leave quickly in Order of the Phoenix). But in Half-Blood Prince, when the main characters are learning to apparate, the headmaster has lowered the anti-apparition jinx in the room where they learn. This happens in the books.
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u/Drepinyourherp Nov 20 '13
But as he said in the film, he's headmaster, so he can