Let me put this in a speculation type post:

If we assume Bahamut is a Primal or was at least feeding off his prison of Dalamud, what happened when we defeated Ifrit, Garuda and Nael van Darnus? Dalamud absorbed their power. What if the Primals act as a means of keeping Bahamut weak within Dalamud. Splinters of his power that keep him contained, and we freed just enough to give him the strength to resist?

He didn't break out of the seal because the Twelve were weaker.
He broke out of the seal because we made him stronger...