### 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)

mesh = src_mesh_node->get_mesh()->get_mesh();
			}
			if (mesh.is_valid()) {
				mesh_node->set_mesh(mesh);
				for (int i = 0; i < mesh->get_surface_count(); i++) {
					mesh_node->set_surface_override_material(i, src_mesh_node->get_surface_material(i));
				}
			}
		}
		switch (p_light_bake_mode) {
			case LIGHT_BAKE_DISABLED: {
				mesh_node->set_gi_mode(GeometryInstance3D::GI_MODE_DISABLED);
			} break;
			case LIGHT_BAKE_DYNAMIC: {
				mesh_node->set_gi_mode(GeometryInstance3D::GI_MODE_DYNAMIC);
			} break;
			case LIGHT_BAKE_STATIC:
			case LIGHT_BAKE_STATIC_LIGHTMAPS: {
				mesh_node->set_gi_mode(GeometryInstance3D::GI_MODE_STATIC);
			} break;
		}
		p_node->replace_by(mesh_node);
		memdelete(p_node);
		p_node = mesh_node;
	}
	for (int i = 0; i < p_node->get_child_count(); i++) {
		_generate_meshes(p_node->get_child(i), p_mesh_data, p_generate_lods, p_create_shadow_meshes, p_light_bake_mode, p_lightmap_texel_size, p_src_lightmap_cache, r_lightmap_caches);
	}
}
void ResourceImporterScene::_add_shapes(Node *p_node, const Vector<Ref<Shape3D>> &p_shapes) {