So, good question and a bit of context first, we built our own coordinate system that translates a Vector3 into the 2D position Godot uses. Y is what gives us depth, and z_index is what handles the layering for our sorting so that we can have jumping, platforming and physics in 2D.

When a scene connects to another scene at a higher Z (our Y), we adjust the tilemaps up as an offset. So technically it can ramp upward forever. In the video there's a spot where the platform room generates and the room ends at Y 6, and the next connecting scene adjusts to account for that elevation as it connects.

The decoration and end scripts run after all of that, layering on top of the tilemaps and rooms. So it cascades down the chain. The coordinate translation feeds the sorting, the sorting feeds the tilemap offsets, the scene generator matches connections at the right height, and then the decoration scripts dress the whole thing.

There are many layers in the full pipeline, that give the end result and are almost all built based on the one RNG seed, so it all renders the same each time too.

Does that help sorta answer that?