Star Grinch wrote:

which by the name would presumably be in the Atlantic Ocean
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The Azores Plateau (aka The Dolphin Plateau) of the Mid-Atlantic Ridge would seem to be what the episode said was going to be the site of the Atlantis Project. Parts of this plateau are over a kilometre down, but the tallest bit is over 2 kilometres above the ocean surface, in the Azores Islands.

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Sure it would displace a ton of water. But I would think a society with transporters and entire weather control systems could get around that problem easy enough.
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The big problem I see is the blocking of the ocean current that flows from the Caribbean toward northern Europe. Without weather control, Europe is going to get very cold.