Oh, really? I misunderstood that part then. Okay, that works too.
The point is that unless a future Xenoblade game decides to retcon it, it's pretty clear that Alvis is meant to be the missing Aegis regardless of any nitpicky details.
If I'm not missing any details, I think this is the general order of events in Alrest:
1. Ontos, Logos, and Pneuma are trinity processors that communicate directly with the Conduit on the First Low Orbit Station
2. Klaus activates the Conduit and creates a new universe, leaving the original universe destroyed
3. Ontos vanishes from the original universe while Logos and Pneuma remain in the original universe
4. Much later in the original universe, Klaus creates the Blade system and reformats Logos and Pneuma as Aegises to oversee the Blade system.
5. Much later in the original universe, Amalthus climbs the world tree and takes the reformatted Logos and Pneuma. Amalthus bonds with Logos' core crystal and Malos awakens.
6. In the original universe, Addam bonds with Pneuma's core crystal and Mythra awakens
If Ontos is Alvis, the general sequence of events for the Xenoblade 1 universe would probably be the following:
1. Ontos, Logos, and Pneuma are trinity processors that communicate directly with the Conduit on the First Low Orbit Station
2. Klaus activates the Conduit and creates a new universe, leaving the original universe destroyed
3. Ontos vanishes from the original universe and enters the new universe the Conduit created. Since Ontos vanishes before Klaus begins working on the Blade system in the original universe, Ontos is never reformatted into an Aegis and continues to exist as a trinity processor. At some point in time in the new universe, Ontos takes on the name Alvis.
4. Zanza and Meyneth awaken as the souls of the Bionis and the Mechonis. From there, the backstory of Xenoblade 1 plays out.