As a form of apologetics, how about “gather all the animals” meant all the livestock; cattle, chickens, goats, horses, enough to propagate after the flood, where otherwise they’d be lost and jeopardize their ability to survive? The flood covered “their world” the area inherited from their ancestors. 40 days may have been their way of saying “awhile”. An ark might be large enough for that and food. The “ark” might not even need to float, just walls, maybe no keel, just enough to keep out the flood waters.