The final fight in the engineering hull would indicate that both sides could get to the engine room uncontested.
It could mean that someone involved behind the scenes thought the Engineering set lived in the saucer right in front of the impulse engines. In which case we might go ahead and speculate there is an engineering-like area right about there.
OTOH, at the end of the episode, we see the pinwheel of doom fly away into space from roughly the middle of the ship's second hull, which would seem to indicate that someone involved behind the scenes did indeed think the engineering set was down there after all.
I figure the majority of the hull's pressure compartments were rendered inescapable by the evil pinwheel but the ship's vital areas were still connected by unaffected areas. This way, a path can indeed be traced from the bridge to the Engineering Room down in the Engineering Section, and the 300+ other Enterprise
crew were indeed
trapped in the sense that they were trapped in whatever pressure compartment they happened to be in when this whole pinwheel affair began.
That's my take on it anyway.