Generally, these spaces are protected with either Low Pressure CO2 or in some cases a foam smothering system. My guess here is a CO2 system that wasn't used or effective because there were no boundaries keeping the CO2 in the space because cargo hold water-tight doors were open- or the ship was ventilating the holds to remove smoke/heat to be able to see. Just a guess.
You make some excellent points and unfortunately they were deadly to some brave men. Access to extinguish ignition points is not as easy as breaking a window or cutting a hole in a roof. It is a very different beast. Thank you for sharing your knowledge.