Locking up 400 people while letting Kirk and a few dozen of his friends roam the bridge, the armory, the sickbay and warp engineering... You simply can't do that by drawing a simple plane across the ship, dividing it to "locked half" and "free half". Most of the people would be in the saucer anyway, so even the area of the impulse engines would be out of Kirk's reach if half his people really sat behind a simple dividing plane.
And as soon as we start to accept that the lock-up pattern was complex, we may just as well go all the way and accept that we cannot tell where the various locations were within the ship in "Day of the Dove". Not by the corridor shots and the dialogue alone. Engineering could be next to the impulse engines, or in the secondary hull, or up in one or both of the nacelles, or perhaps directly below the bridge.
What the dialogue does tell us is that the Klingons are in control of the ship at "deck 6 and starboard deck 7", while the heroes control "all sections above". Now that would suggest that somebody is disputing the Klingon control of portside deck 7. Is that the alien, preventing access to lower decks? Or is that Kirk, preventing access to the upper ones? After all, we have no reason to think the writer of this particular episode would have intended the deck numbers to grow from top towards the bottom...
Then again, other writers usually seemed to think that the numbers grew from top to bottom. I see no possibility of solving this one way or another by tweaking with the visuals alone. Not unless the scene where the alien departs is filmed as a massive zoom-out through the hull, showing the starting point of that curvy path in detail, inside the ship!
Timo Saloniemi