Scene Composition Issues: Object Floating, Scaling Mismatch, and Interpenetration in InternScenes_Real2Sim

First of all, thank you for the impressive work on the InternScenes pipeline!
While using the InternScenes_Real2Sim pipeline to generate composed scenes, I encountered several physical and layout consistency issues in some scenes, I have categorized the issues into four main types: Object Interpenetration, Incorrect Scaling, Floating Objects, and Anomalous Layout Logic (Room-in-Room).

Scene ID: 3rscan / 5341b7d9-8a66-2cdd-844b-cfdadb69ed63
Problem: The generated layout shows a smaller room structure incorrectly placed inside a larger room, leading to a redundant or nested wall structure that doesn't match the actual scan.

Scene ID: 3rscan / 5341b7d9-8a66-2cdd-844b-cfdadb69ed63
Problem: Multiple objects are overlapping or clipping through each other, which violates physical constraints for Real2Sim tasks

Scene ID: arkitscenes / Training / 41125501
Problem: Certain CAD models are scaled incorrectly relative to the environment. For example, a cup appears significantly larger than its real-world counterpart.

I noticed that while some rooms are generated perfectly, others appear cluttered or physically implausible. I would like to clarify:
Are these issues primarily caused by noisy annotations/layouts in the original source datasets?
Or is there a potential bug in the CAD model matching or Z-axis heuristic alignment code within the pipeline?
Are there any recommended parameters or post-processing scripts (like collision check/gravity settling) to mitigate these messy layouts?

Start by reproducing the InternScenes_Real2Sim outputs for the supplied 3rscan and arkitscenes scene IDs. Inspect the CAD model matching and Z-axis heuristic alignment against the source annotations and layouts, then determine whether the reported nesting, overlap, and scaling issues come from the data or pipeline; document a reproducible cause and any validated mitigation.