The claim that Noah’s Ark was pyramidal in shape shouldn’t be a shock to fringe writers. It’s in fringe literature, typically as part of a conspiracy theory. For example, Scott Creighton described it in his book The Secret Chamber of Osiris (2015) in which he imagined that the pyramid-shaped ark on the doors of the Florentine Baptistery’s Gates of Paradise by Lorenzo Ghiberti was secretly depicting Khufu’s pyramid. Ramesh Ramsahoye wrote an article about the same piece of art in UFO Magazine in September 2003, where he claimed that Graham Hancock’s research helped him to realize that Noah’s Ark was really the Great Pyramid of Giza, and that it must have contained secret knowledge from before the Flood.
The story of Noah placing two of 'every living thing' within the Ark could be a poetic metaphor for 'everything being stored inside'. If an advanced civilisation knew that it was going to be devastated by an impending catastrophe, then it would make perfect sense to attempt to preserve its scientific knowledge and culture.
What is especially interesting is that Ancient Origins actually used pictures of Ghiberti’s work to illustrate the story, seemingly without curiosity as to what Ghiberti depicted and why.
Ghiberti was actually depicting a widespread Jewish and early Christian belief about the Ark. Origen, in Genesis Homily 2, Philo in Questions and Answers on Genesis 2.5, and Clement in Stromata 6.11 all claimed that the Ark was pyramidal in shape. They derived this from the account in Genesis, which claimed that the Ark is 300 by 50 cubits at the base, but rose to a window embedded in a peak but one cubit square. They concluded, therefore, that the ship must be pyramidal to fit those measurements.
The Dead Sea Scrolls were deposited, scholars believe, between 300 BCE and 100 CE, overlapping the time when Philo was active and therefore proving that the belief was widespread enough to have popped up in multiple places around the ancient Judeo-Christian world. In other words, the Dead Sea Scrolls did not reveal a “new” interpretation of Noah’s Ark at all.
The claim that the Ark was pyramid-shaped had an unusual side effect. It must have led Late Antique Coptic Christians to try to explain why Egypt’s pyramids bore the same shape as the Ark. It is quite possible that this was one reason that the earlier legend that Hermes had encoded secret knowledge into the temples of Egypt to guard against the prophesied destruction of the Earth by fire and flood transformed into the idea that scientific knowledge had been saved from Noah’s Flood in stone versions of Noah’s Ark. The story then passed into the hands of the medieval Arab scholars. Ibrahim ibn Wasif Shah, the medieval writer quoted by al-Maqrizi, makes this connection rather clear when he parallels Surid’s efforts to save knowledge inside the pyramids with the Egyptian priest Philemon’s efforts to save people from the flood by finding Noah’s Ark. “Yes, whoever wants to be saved must go to reach the master of the Ark,” angels are made to say to Philemon.