It's possible Allag invaded Ayatlan at some point and unleashed the 'Lord of Snakes' on the Ixal before they summoned Garuda to defeat him and lost their wings in the process. Those imprisoned in what I assume to be a lab of some kind were likely taken for genetic experimentation.
There's another possibility though and that's that the Allagans actually created the Ixal. One of Midgardsormr's seven sons has a beak and horns identical to those of the Ixal and I would not be surprised to discover that they are the results of genetic experimentation on him. The dreadknights in the binding coil could very well be the culmination of that research and the Ixal we know in Eorzea escaped the Floating Continent at some point and fled to the ground below. If this were the case then the creature bound within that sphere may well be the dragon they were created from.
I have been considering the possibility that the second of those Allagan dungeons actually is the ruin that Omega is held in under Cartenau. Again I'm not sure why he'd be held in some kind of prison but I suppose it's entirely possible. The architecture there matches what we've seen of the Floating Continent though so I'm leaning more to that being the likely location.
