### 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)

md.has_import_id = has_import_id;
		md.material = p_material;
		_load_default_subresource_settings(md.settings, "materials", import_id, ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MATERIAL);
		material_map[import_id] = md;
	}
	MaterialData &material_data = material_map[import_id];
	Ref<Texture2D> icon = get_theme_icon(SNAME("StandardMaterial3D"), SNAME("EditorIcons"));
	TreeItem *item = p_tree->create_item(p_parent);
	if (p_material->get_name().is_empty()) {
		item->set_text(0, TTR("<Unnamed Material>"));
	} else {
		item->set_text(0, p_material->get_name());
	}
	item->set_icon(0, icon);
	item->set_meta("type", "Material");
	item->set_meta("import_id", import_id);
	item->set_tooltip_text(0, vformat(TTR("Import ID: %s"), import_id));
	item->set_selectable(0, true);
	if (p_tree == scene_tree) {
		material_data.scene_node = item;
	} else if (p_tree == mesh_tree) {
		material_data.mesh_node = item;
	} else {
		material_data.material_node = item;
	}
	if (created) {
		_fill_material(material_tree, p_material, material_tree->get_root());
	}
}
void SceneImportSettings::_fill_mesh(Tree *p_tree, const Ref<Mesh> &p_mesh, TreeItem *p_parent) {