Complex sentence: For safety and to avoid confusion this "hole" was below the level of the flight deck, though may not have been an actual pit on older carriers, might have been just a designated off-the-flight-deck spot the pilot would await.
Split into simpler sentences: For safety and to avoid confusion this "hole" was below the level of the flight deck. On older carriers, it may have been an actual pit or just a designated off-the-flight-deck spot the pilot would await.