That's exactly what makes me think that Midgardsormr was originally intended to be the identified threat and SE is backing it up a little. Garlemald did bring in the big guns... and sailed it directly to Midgardsormr. Assume it was any other primal and try to make sense of it. Doesn't matter which - even an imaginary one. What reason would they have to assume they'd need to send the Agrius to take Mor Dhona in case the move angered... Titan? or Ramuh? or Ifrit?
This is no longer true. It's been stated that the Empire faced primals on the other continents on their new official site.
EDIT: "The eastern nations were the first to feel the newborn empire's mighty fist. It was during this campaign that the emperor witnessed firsthand the destruction wrought by the primals―an experience that led to an imperial mandate for their annihilation."
It would give them access to commune with it, to worship it and receive its guidance, maybe even some sort of blessings via interdimensional medium, who knows. However, the primals don't want communication, they want Aether Snacks and corporeal form - that's what would take being fed a lot more aether.
What I'm saying is that maybe the initial burst of aether from the broken seal was able to give them a little taste of what it is they're after - and that, while I'm not propagating this as a theory, it is the only thing I can think of to justify the original intent of saying "the unexpected appearance of a primal didn't mean Midgardsormr.
Let's not forget, I could be totally wrong here. Much like how all it took was the concept of a "seal" on Mor Dhona to constrain us before, there could be a simple missing puzzle piece that we haven't been given yet. Maybe Ala Mhigo had a primal that we haven't been told about yet - maybe it was worshipped by a beast tribe we haven't seen yet. We simply don't know.
It just seems odd to me that information from the very beginning only meshes about 75% with the information we have now, barring a missing puzzle piece, unless there's a clever retcon in place that just needs a little frayed-end clipping.