That's a very interesting idea, and it does make sense. However, that would mean that a most monumental aspect of Eternian history is yet to be revealed. And it would have to be one hell of a threat for those three to feel the need to band together just to fight it.
I think what is hinted at is that at this point in Eternian history, all three were so evenly matched that it was like a mutual destruction pact, kind of like our Cold War of the 20th century. No open hostilities, but plenty of behind the scenes action. Perhaps the Three Towers even had a political meaning, much like the United Nations. I tend to favor this idea, rather than some massive threat that has been hitherto unknown, and left out.