Ark Royal's problems didn't lie in the boiler rooms but in the space above that contained the boiler uptakes that carried the boiler gases across the ship to the funnel. That arrangement allowed gradual flooding of the centre and then port boiler rooms, as she listed to starboard and sank lower in the water. Her loss revealed the problem.But yes, more Ark Royal with modifications to sub-divide the boiler rooms would have been better.
The same design was used in the Illustrious class. A fix was applied to them as they came in for refit or repair from 1942. That involved half height bulkheads being installed in the spaces concerned. The problem was caught early enough to allow the modification of the Audacious class design to carry the boiler uptakes higher in the ship before moving them across the ship.