I tested the updated GLB in a completely fresh Godot 4 project. The issue is still present.
The GLB itself still contains non-unit scales on mesh nodes. For example, the Stairs node is exported with:
"scale": [0.149999991, 0.085000001, 0.344688237]
Godot is importing the file correctly; these values are already present in the GLB.
Could you check why the exporter is writing non-unit node scales instead of baking the transforms into the mesh geometry? Ideally, each exported mesh node should have a local scale of (1,1,1).
Thank you for having a look!