Mystery Babylon was a mystery to the the Church because it would dominate the Earth from a place that had not yet entered the imagination of the Old World. The description of the Great City she manifest in as being free from the threat of invasion, at the center of global maritime trade and between two rivers is a clue to Babylon's orientation on the globe at this specific time. The emergence of the spirit of Babylon in North America during the 1880's(The Great Melting Pot) could only be realized in the post-modern era. As well as the immense power, wealth, luxury and commerce she acquired after defeating the emperors of the Old World. Today she is a stumbling block to the unification of Eurasia. While she brings a world war to their doorstep policing a world restless to break free from the tired New Order she imposed upon them, becoming more desperate to divorce her with each passing year.
Associating the meaning of the word "mystery" with religion worked in the 10th century when Holy Rome dominated Europe. This view does not hold water at the End Times. It fails to recognize Holy Rome's ultimate destruction by Napoleon and the military frailty and low population of the European Union in the face of Russia, China, India and the United States.