### Godot version

4.0 beta 15

### System information

Windows 10

### Issue description

When ticking `apply_root_scale` the scale is not applied to custom collision shape set in importer.
This apply for `shape_type`  Box, Sphere, Cylinder and Capsule

_I tried to fix it myself but i'm a bit confused on how to have acces to the `apply_root_scale` and `root_scale` at the moment where the shape is generated_

### Steps to reproduce

- Add a 3d model.
- Generate physics for the mesh
- Select a `shape_type` for example Box
- Add `root_scale` != 1 and tick `apply_root_scale`

### Minimal reproduction project

[BoxColliderImport.zip](https://github.com/godotengine/godot/files/10500751/BoxColliderImport.zip)

} else {
						mi->add_child(nmi, true);
						nmi->set_owner(mi->get_owner());
					}
				}
			}
		}
	}
	if (Object::cast_to<ImporterMeshInstance3D>(p_node)) {
		ImporterMeshInstance3D *mi = Object::cast_to<ImporterMeshInstance3D>(p_node);
		Ref<ImporterMesh> m = mi->get_mesh();
		if (m.is_valid()) {
			if (node_settings.has("generate/occluder")) {
				int occluder_mode = node_settings["generate/occluder"];
				if (occluder_mode != OCCLUDER_DISABLED) {
					float simplification_dist = 0.0f;
					if (node_settings.has("occluder/simplification_distance")) {
						simplification_dist = node_settings["occluder/simplification_distance"];
					}
					OccluderInstance3D::bake_single_node(mi, simplification_dist, r_occluder_arrays.first, r_occluder_arrays.second);
					if (occluder_mode == OCCLUDER_OCCLUDER_ONLY) {
						memdelete(p_node);
						p_node = nullptr;
					}
				}
			}
		}
	}
	if (Object::cast_to<AnimationPlayer>(p_node)) {
		AnimationPlayer *ap = Object::cast_to<AnimationPlayer>(p_node);