I have given this some more thought in light of the advice and suggestions given, and I have now decided upon a third alternative.

The layout I currently have in mind focuses on providing three distinct floors throughout the level. I am planning on going for the "preserved" approach for the foundations, the "ruined" art style for the upper regions, and a new "destroyed" appearance (not actually using floors, simulating a gigantic ripped-apart layer) for occasional passages in between.

I see this approach as suitable, given the plausibility of such a scenario: as this is a Sunken City, the foundations could have dropped to an extent and preserved the lower halls, leaving any higher ground ruined and haphazard due to a lack of support from beneath, having a side effect of the rock in between occasionally breaking apart and leaving a destroyed tunnel separating the two. The last point listed here could also account for occasional pits scattered throughout the lower floor.

What do you all think?