The Ark is more than twice as long and more than four times as wide as the island of Manhattan, and higher than Mount Everest. From what we have seen, it must have several decks - the inside shots we got of it when Imakarum travelled through it suggests those decks are no more than perhaps a hundred meters high. That means you could comfortably stack at least twenty of those.
Also I found the relevant page...
A million seems needlessly conservative. If we are talking about twenty habitable decks, each, say, twenty kilometers long (less than 40% of the total length of the ship) and, say, three kilometers wide, that's 1200 square kilometers - a little larger than Hong Kong, which has over seven million citizens.