### 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)

ResourceImporterScene *ResourceImporterScene::scene_singleton = nullptr;
ResourceImporterScene *ResourceImporterScene::animation_singleton = nullptr;
Vector<Ref<EditorSceneFormatImporter>> ResourceImporterScene::importers;
Vector<Ref<EditorScenePostImportPlugin>> ResourceImporterScene::post_importer_plugins;
bool ResourceImporterScene::ResourceImporterScene::has_advanced_options() const {
	return true;
}
void ResourceImporterScene::ResourceImporterScene::show_advanced_options(const String &p_path) {
	SceneImportSettings::get_singleton()->open_settings(p_path, animation_importer);
}
ResourceImporterScene::ResourceImporterScene(bool p_animation_import) {
	if (p_animation_import) {
		animation_singleton = this;
	} else {
		scene_singleton = this;
	}
	animation_importer = p_animation_import;
}
void ResourceImporterScene::add_importer(Ref<EditorSceneFormatImporter> p_importer, bool p_first_priority) {
	ERR_FAIL_COND(p_importer.is_null());
	if (p_first_priority) {
		importers.insert(0, p_importer);
	} else {
		importers.push_back(p_importer);
	}
}
void ResourceImporterScene::remove_post_importer_plugin(const Ref<EditorScenePostImportPlugin> &p_plugin) {
	post_importer_plugins.erase(p_plugin);
}
void ResourceImporterScene::add_post_importer_plugin(const Ref<EditorScenePostImportPlugin> &p_plugin, bool p_first_priority) {