Or we can take some creative license that the death room was more at the bottom of the shaft, tying into the base of the reactor. The dramatic intent is the same - it's down the long energizer shaft, in the bowels of the ship, in engineering. It doesn't NEED to be at the horizontal and vertical intersection (though that's what's on screen).
"If you need a holodeck to make an interstellar starship on the bleeding edge of the unknown
interesting, something is seriously amiss."
- Straczynski & Zabel