diff --git a/src/scene_synthesizer/assets.py b/src/scene_synthesizer/assets.py
index c5d8f32..1636985 100644
--- a/src/scene_synthesizer/assets.py
+++ b/src/scene_synthesizer/assets.py
@@ -1310,7 +1310,7 @@ def _usd_prim_path_to_node_name(path):
                 else:
                     matrix = transform_A @ transform_B
 
-            log.debug(f"Adding {parent_path} ({parent_node_name})--> {xform_path} ({node_name})")
+            log.debug(f"Adding {parent_path} ({parent_node_name})--> {xform_path} ({node_name}) with transform={matrix}")
             utils.add_node_to_scene(
                 scene=s,
                 node_name=node_name,
@@ -1357,18 +1357,17 @@ def _usd_prim_path_to_node_name(path):
                 fname=self._fname,
                 file_element=mesh_prim.GetPath().pathString,
             )
-
-            scale = usd_import.get_scale(mesh_prim)
-            if not np.allclose(scale, [1.0, 1.0, 1.0]):
-                geometry.apply_scale(scale)
-            
-            # Store the original mesh exents, note that this *includes* the file-specific
+            # Store the original mesh exents, note that this does *not* include the file-specific
             # scaling factor. During reference-based export we will use this information
             # to infer any additional necessary scaling factor.
-            # Note: There might be a use case in which storing the extents *before* scaling
+            # Note: There might be a use case in which storing the extents *after* scaling
             # the geometry is helpful.
             utils.add_extents_to_trimesh_metadata(mesh_or_scene=geometry)
 
+            scale = usd_import.get_scale(mesh_prim)
+            if not np.allclose(scale, [1.0, 1.0, 1.0]):
+                geometry.apply_scale(scale)
+            
             node_name = _usd_prim_path_to_node_name(mesh_path)
             parent_node_name = _usd_prim_path_to_node_name(mesh_prim.GetParent().GetPath())
             if _usd_prim_path_to_node_name(mesh_prim.GetParent().GetPath()) not in s.graph.nodes:
diff --git a/src/scene_synthesizer/exchange/usd.py b/src/scene_synthesizer/exchange/usd.py
index 889b591..ad5a00d 100644
--- a/src/scene_synthesizer/exchange/usd.py
+++ b/src/scene_synthesizer/exchange/usd.py
@@ -822,46 +822,56 @@ def add_joint_to_usd(
             if object_name in referenced_stages
             else get_stage(referenced_stage_fnames[object_name])
         )
-
-        referenced_stage_scaling_factor = (
-            get_meters_per_unit(referenced_stage) / stage_meters_per_unit
-        )
+        stage_will_be_written = bool(object_name in referenced_stages)
         
-        geom_scales = []
-        for object_geom_node_name in scene.get_geometry_names(object_name):
-            object_geom_name = scene.graph.transforms.node_data[object_geom_node_name]['geometry']
-            if "extents" in scene.geometry[object_geom_name].metadata:
-                geom_scales.append(
-                    scene.geometry[object_geom_name].extents
-                    / scene.geometry[object_geom_name].metadata["extents"]
-                )
-        geom_scales = np.array(geom_scales)
-        
-        # check if consistent
-        if len(geom_scales) > 0:
-            if not np.allclose(geom_scales - geom_scales[0], 0, atol=1e-4):
-                log.warning(
-                    f"Geometries of referenced USD asset have different scales. Won't apply any"
-                    f" scaling. Result maybe wrong."
-                )
-            else:
-                if np.allclose(geom_scales[0] - geom_scales[0][0], 0.0):
-                    # scalar scale
-                    referenced_stage_scaling_factor *= geom_scales[0][0]
-                else:
-                    # vector scale
-                    referenced_stage_scaling_factor = (
-                        geom_scales[0] * referenced_stage_scaling_factor
+        referenced_stage_scaling_factor = None
+        if not stage_will_be_written:
+            referenced_stage_scaling_factor = (
+                get_meters_per_unit(referenced_stage) / stage_meters_per_unit
+            )
+            
+            # Determine how much the geometry is scaled w.r.t. to its initial size
+            geom_scales = []
+            for object_geom_node_name in scene.get_geometry_names(object_name):
+                object_geom_name = scene.graph.transforms.node_data[object_geom_node_name]['geometry']
+                if "extents" in scene.geometry[object_geom_name].metadata:
+                    geom_scales.append(
+                        scene.geometry[object_geom_name].extents
+                        / scene.geometry[object_geom_name].metadata["extents"]
                     )
         
+            geom_scales = np.array(geom_scales)
+            
+            # check if consistent
+            if len(geom_scales) > 0:
+                if not np.allclose(geom_scales - geom_scales[0], 0, atol=1e-4):
+                    log.warning(
+                        f"Geometries of referenced USD asset have different scales. Won't apply any"
+                        f" scaling. Result maybe wrong."
+                    )
+                else:
+                    if np.allclose(geom_scales[0] - geom_scales[0][0], 0.0):
+                        # scalar scale
+                        referenced_stage_scaling_factor *= geom_scales[0][0]
+                    else:
+                        # vector scale
+                        referenced_stage_scaling_factor = (
+                            geom_scales[0] * referenced_stage_scaling_factor
+                        )
+            
+            # If 1.0 set to None
+            if np.allclose(referenced_stage_scaling_factor, 1.0):
+                referenced_stage_scaling_factor = None
+
+        # TODO(ceppner): does not scale the articulation units
         scene_path = scenegraph_to_usd_primpath[object_name]
+        # Note: This overwrites the transform/scale in the
+        # referenced file.
         prim = usd_export.add_xform(
             stage=stage,
             scene_path=scene_path,
             transform=referenced_stage_transforms[object_name],
-            scale=referenced_stage_scaling_factor
-            if not np.allclose(referenced_stage_scaling_factor, 1.0)
-            else None,
+            scale=referenced_stage_scaling_factor,
         )
 
         if scene.is_articulated(object_name):