Observations:
Lavos' shell is surrounded by a shimmering blue field when it is confronted during the ocean palace disaster and any other time it is fought.
Lavos's abilities and state of being is static in all cases (1999 A.D., Black Omen routes), save for the Ocean Palace battle.
Lavos shell is visible from the ground, without any surrounding field, while the travellers approach in 1999 AD. The travellers appear in the blue field when they confront Lavos.
I just defeated Lavos in the Ocean Palace, and left through the Gate. Coming to 1999 A.D., he erupts from the ground, and it briefly shows the blue background with his head gone and a hole there. When the party truly approaches him, he is on the ground normally, with no blue field (head still gone).
From the "air" Lavos is observed to impact the earth, erupt to destroy Zeal in 12000 BC and erupt to destroy the world in 1999 AD, without any blue field.
If the bucket or Epoch is used to reach Lavos, it is approached in 1999 AD.
The Lavos core engages the party in a temporal flux sort of arena, in which time periods are at its fingertips. Specifically: Prehistoric (appears like 65 million BC), Zeal (appears like 12000 BC), Middle Ages (appears like 600 AD), "Present" (appears like 1000 AD), "Ruined Future" (appears like 2300 AD). "Time Warp" is displayed when the time periods shift. Lavos attacks correspond to the time periods which are displayed.
When the Black Omen is defeated in any era, it is destroyed by a energy beam originating from within the earth.
When the Omen is gone, Lavos erupts. No landforms at all, just a simple ocean graphic.
The Mammon Machine is damaged in the real world, but inside the same blue background, it is unharmed.
If Lavos' shell is defeated, it will still be defeated at any other time, except for the Ocean Palace disaster.
Lithosphere Investigation Report clearly shows him in the real world. Like the "aerial" view on the world map or Day of Lavos record.
Problems
Defeating Lavos inside the pocket dimension prevents the Day of Lavos, but not the destruction of Zeal or any of Lavos' other effects on the earth.
If Lavos' shell is defeated, it will still be defeated at any other time, except for the Ocean Palace disaster, which appears to be an inconsistency.