The script, as many do, went through a number of revisions and rewrites including being completely scrapped and used for parts.
The reference to the 12 pages, per a link at Wikipedia, is made in The Greatest Science Fiction Movies Never Made (p33) by David Hughes but does not contain any specific information.
EDIT: from Forgotten Trek
Later Khan and Kirk would fought [sic] a psychic battle in a variety of exotic locations, using quarterstaffs, whips and swords. Khan, who had acquired impressive mental powers during his isolation, eventually won but Kirk survived because he understood that the weapons were only illusory.
From Wikipedia.
[Harve] Bennett wrote his first film treatment in November 1980. In his version, entitled The War of the Generations, Kirk investigates a rebellion on a distant world and discovers that his son is the leader of the rebels. Khan is the mastermind behind the plot, and Kirk and son join forces to defeat the tyrant. Bennett then hired Jack B. Sowards, an avid Star Trek fan, to turn his outline into a film-able script. Sowards wrote an initial script before a writer's strike in 1981. Sowards' draft, The Omega Syndrome, involved the theft of the Federation's ultimate weapon, the "Omega system". Sowards was concerned that his weapon was too negative, and Bennett wanted something more uplifting "and as fundamental in the 23rd century as recombinant DNA is in our time", Minor recalled. [Michael] Minor [Art Director] suggested to Bennett that the device be turned into a terraforming tool instead. At the story conference the next day, Bennett hugged Minor and declared that he had saved Star Trek. In recognition of the Biblical power of the weapon, Sowards renamed the "Omega system" to the "Genesis Device".
April 1981, Sowards had produced a draft that moved Spock's death to later in the story, because of fan dissatisfaction to the event after the script was leaked. Spock had originally died in the first act, in a shocking demise that Bennett compared to Janet Leigh's early death in Psycho. This draft had a twelve-page face-to-face confrontation between Kirk and Khan Sowards' draft also introduced a male character named Saavik. As pre-production began, Samuel A. Peeples, writer of the Star Trek episode "Where No Man Has Gone Before", was invited to offer his own script. Peeples' draft replaced Khan with two new villains named Sojin and Moray; the alien beings are so powerful they almost destroy Earth by mistake. This script was considered inadequate; the aliens resembled too closely the villains on a typical TOS episode. Deadlines loomed for special effects production to begin (which required detailed storyboards based on a completed script), and by this point there was no finished script to use.
Director Nicholas Meyer had never seen an episode of Star Trek when approached to direct the film and rewrite the script.
Karen Moore, a Paramount executive, suggested to Bennett that Nicholas Meyer, writer of The Seven-Per-Cent Solution and director of Time After Time, could help resolve the screenplay issues. Meyer had also never seen an episode of Star Trek. He had the idea of making a list consisting of everything that the creative team had liked from the preceding drafts —"it could be a character, it could be a scene, it could be a plot, it could be a subplot, [...] it could be a line of dialogue"—so that he could use that list as the basis of a new screenplay made from all the best aspects of the previous ones. To offset fan expectation that Spock would die, Meyer had the character "killed" in the Kobayashi Maru simulator in the opening scene. The effects company required a completed script in just 12 days. Meyer wrote the screenplay uncredited and for no pay before the deadline, surprising the actors and producers, and rapidly produced subsequent rewrites as necessary. One draft, for example, had a baby in Khan's group, who is killed with the others in the Genesis detonation....
Kirk and Khan never confront each other face-to-face during the film. All of their interactions are over a viewscreen or through communicators and their scenes were filmed four months apart, although a draft script had Khan defeating Kirk in a swordfight.
Meyer described Shatner as an actor who was naturally protective of his character and himself, and who performed better over multiple takes.
12 pages in a script usually equates to, I believe, about 12 minutes of screen time...that's a long time for a "confrontation"...even if a swordfight (sigh) was involved.
It appears that Meyer took the bits of the script he liked, knew his actors' strengths and weaknesses and made the right choices.
