When you're dealing with a very powerful entity that can reshape an entire continent by being alive for only a few minutes (a few seconds in the trailer), you'd want something to counter it should it ever break free. I'm not arguing against the possibility that the Omega weapon was used to cage him the first time, but I don't think its existence outright confirms that it was ever used. In fact, it could very well be a combination of both theories since they could have created Bahamut through their "fake prayer techology" and have had the Omega weapon suppress the elder primal while they were binding it to Dalamud.

It just seems unlikely that Bahamut was a free-roaming creature during the Allag's age and prior without any mention of its existence by any other culture. You'd think we'd come across a temple dedicated to him or at least a painting on a wall of people fleeing the thing in terror.