Yes, but that does not mean Dalamud can't bring it forth from below the lake. I really think this theory is plausible. Just imagine the possibilities of the top floor of the Crystal Tower being Dalamud. Current players will know the entire history of the formation of the Crystal Tower. I think that would be very cool.

"I wonder how this tower got here"

"We made it happen, by stopping the Empire in the 6th Astral Era."