I certainly don't understand the point Cracked is trying to make about their link to a passage in the Timaeus demonstrating that Atlantis is completely hypothetical. The quote they try to link to comes from an explanation by Critias that a real, non-hypothetical city of Atlantis which the people of Athens once fought happen to have fit the bill of the idealized city to which Socrates refers.

Critias:

And when you were speaking yesterday about your city and citizens, the tale which I have just been repeating to you came into my mind, and I remarked with astonishment how, by some mysterious coincidence, you agreed in almost every particular with the narrative of Solon...

and the narrative of Solon to which he refers:

But one of them exceeds all the rest in greatness and valour. For these histories tell of a mighty power which unprovoked made an expedition against the whole of Europe and Asia, and to which your city put an end. This power came forth out of the Atlantic Ocean, for in those days the Atlantic was navigable; and there was an island situated in front of the straits which are by you called the Pillars of Heracles; the island was larger than Libya and Asia put together, and was the way to other islands, and from these you might pass to the whole of the opposite continent which surrounded the true ocean; for this sea which is within the Straits of Heracles is only a harbour, having a narrow entrance, but that other is a real sea, and the surrounding land may be most truly called a boundless continent. Now in this island of Atlantis there was a great and wonderful empire which had rule over the whole island and several others, and over parts of the continent, and, furthermore, the men of Atlantis had subjected the parts of Libya within the columns of Heracles as far as Egypt, and of Europe as far as Tyrrhenia. This vast power, gathered into one, endeavoured to subdue at a blow our country and yours and the whole of the region within the straits; and then, Solon, your country shone forth, in the excellence of her virtue and strength, among all mankind. She was pre-eminent in courage and military skill, and was the leader of the Hellenes. And when the rest fell off from her, being compelled to stand alone, after having undergone the very extremity of danger, she defeated and triumphed over the invaders, and preserved from slavery those who were not yet subjugated, and generously liberated all the rest of us who dwell within the pillars. But afterwards there occurred violent earthquakes and floods; and in a single day and night of misfortune all your warlike men in a body sank into the earth, and the island of Atlantis in like manner disappeared in the depths of the sea. For which reason the sea in those parts is impassable and impenetrable, because there is a shoal of mud in the way; and this was caused by the subsidence of the island.

Socrates, in reply:

And what other, Critias, can we find that will be better than this, which is natural and suitable to the festival of the goddess, and has the very great advantage of being a fact and not a fiction?

In other words, the discussion of the ideal city had been presented as hypothetical right up until the moment WHEN Critias offers the "historical" example of Atlantis. Does it mean Atlantis was real, or that Plato thought it was? Hardly. It reads to me like a conceit to justify the discussion, almost a bit of humour. But it says precisely the opposite of what the Cracked author seems to say it was.

It's certainly possible that there was some Greek myth about a prior civilization to which Critias/Solon refers here; it ties in nicely with the Greek sense of the decline of man through the Golden Age to the contemporary base Iron Age. Such myths could have the barest factual basis in Minoan Crete or, a popular theory, in the island of Thera, although neither of these fits geographically with the description in the Timaeus, so it was certainly highly fictionalized if this is the case. In other words, no one can really say anything terribly conclusive; my objection to the Cracked article is that the point they are trying to make seems to have things totally backwards.

Certainly, Plato is reading a hypothetical "perfect city" into the Atlantis story, but the conceit within the text is that Atlantis is supposed to be a historical example of Plato's ideal.