I recall a comment a long long time ago stating that we would get some kind of explanation on the wider universe of the franchise at some point and that the crossover events would make more sense then.

Given the situation with Iroha now being trapped in our world I'm wondering if she might actually have some significance in the future. It would be entirely possible for the devs to use her character to continue one tiny thread of FFXI's story in FFXIV, since XI's story is now finished.