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If a Dark Apostle or Chaos Lord with the Mark of Tzeentch takes Scrolls of Magnus, he becomes a psyker (as per the FAQ). Now, with Chaos Psychic Focus, he would automatically get the Tzeentch Primaris power. If he chooses to roll once with Scrolls of Magnus, does he get the Discipline Power rolled AND the Discipline Primaris? Or no since he has the Tzeentch Primaris?

He would not because he generated a power that is not from the discipline granted by the Scrolls.

But the Primaris isn't generated (a.k.a. rolled for) as described in The Rules. Only the first power (and subsequent powers) would be.

If he has a mark, then when he becomes a psyker he would qualify for chaos psychic focus and get the primaris of his mark. he would not qualify for regular psychic focus.