I think some things got lost as the story was scripted and finalized.
Here's how the Revised Story Outline for "Survival" (August 8, 1968) describes the situation:
The matter-antimatter control is inoperative; it has been inexplicably and totally destroyed. Scott can fix it, if he begins now... but he might not have enough time. The area where he must work is tight and cramped -- room for just one man. Scott scrambles in and gets to work. The uncontrolled matter-antimatter mixture that provides warp power is almost out of control and will explode in ten minutes -- more or less. At this point, it's impossible to tell -- and just one man can do the job: Scott. Kirk clears the entire "disposable" warp nacelle area, moving all personnel into the saucer section. If they must jettison the nacelles, it is understood by both Scott and Kirk that Scott might not have the time to get out before the thing blows.
And here's how the relevant part appears in the First Draft of "That Which Survives" (September 9, 1968):
INT. CRAWLWAY - CLOSE - SCOTT
SCOTT
All right, Mr. Spock, I'm now opening the access panel to the magnetic flow valve itself. Keep your eye on the dial. If there's a jump in magnetic flow you must jettison me and the entire matter-antimatter nacelle immediately. It will blow in two seconds after the rupture of the magnetic field.
And you know how the above scene wound up in the finished episode.