You could be right. Might be a bit far-fetched, but BS also stated once that he nicknamed Towers of Midnight in his writing process "The Three Towers" for a time. If one takes the Black Tower as a symbol for Rand's power, the White Tower as a symbol for Egwene's power, and the Towers of Midnight as a symbol of Tuon's power, one could also say that these three (towers) become one in an alliance (though one of those "Three Towers" BS meant is rather likely the Tower of Ghenjei).

Anyway, since that Prophecy is such vague, one can't say for sure yet, what any part of it really means. Personally, I tend to think at the moment that it likely refers to Rand & his three ladies, who have something important to do yet, as also various other Prophecies make clear. But I also like the idea that it might refer to the three ta'veren.