Spoilers Obviously
It doesn't, really. It is theorized in the quest that the machine mistook the voidsent for a primal and came to destroy it. It seems convenience-based rather than deep canon; at Fan Fest it took place in Azys Lla on a little island called The Last Remnant.
Honestly it just feels like they killed all the birds with one stone. Missing Proto Ultima FATE, a fight for Fan Fest that wouldn't need to be from scratch, somewhere to stick a 24-man trial where it wouldn't require new systems, gap accessories, and so on.
Lore was probably an after-thought, as it already requires several maybes. Why was Ultima there? Maybe it was trying to kill a primal. How did Ultima mistake a voidsent for a primal? Ehh, something something concentrated aether to manifest something something something very powerful something something it hasn't had a tune-up in 5,000 years. Maybe the goblin is wrong and Ultima also killed uppity Cloud of Darkness minions that grew too powerful and acted outside of certain parameters. "Please just have fun with the fight!" <loosens collar>