because it is the same scene, the origin of both worlds
The Architect of XB2 is Zanza of XB1.
Basically, Professor Klaus initiated the conduit program that wiped out civilization while creating a new universe, but half his body remained in the ruined world which Klaus went on to mold as Alrest/XB2, becoming known as the Architect. The half that the conduit took to the new world of Bionis/Mechonis was Zanza, who became a god with his colleague Professor Galea, Meyneth.
When the Architect says his time is running out, it's because Shulk is about to kill Zanza, when your XB2 party leaves there's even a scene that zooms into the Architect's ruined half / blackhole and you can hear a quote from Shulk in the final battle of XB1.
Unconfirmed Theory: The world beneath the cloud sea at the end of XB2 may actually be the world Shulk created at the end of XB1.