### 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)

if (hide_options) {
			return;
		}
		for (const ResourceImporter::ImportOption &E : options) {
			if (SceneImportSettings::get_singleton()->is_editing_animation()) {
				if (category == ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MAX) {
					if (ResourceImporterScene::get_animation_singleton()->get_option_visibility(path, E.option.name, current)) {
						p_list->push_back(E.option);
					}
				} else {
					if (ResourceImporterScene::get_animation_singleton()->get_internal_option_visibility(category, E.option.name, current)) {
						p_list->push_back(E.option);
					}
				}
			} else {
				if (category == ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MAX) {
					if (ResourceImporterScene::get_scene_singleton()->get_option_visibility(path, E.option.name, current)) {
						p_list->push_back(E.option);
					}
				} else {
					if (ResourceImporterScene::get_scene_singleton()->get_internal_option_visibility(category, E.option.name, current)) {
						p_list->push_back(E.option);
					}
				}
			}
		}
	}
};
void SceneImportSettings::_fill_material(Tree *p_tree, const Ref<Material> &p_material, TreeItem *p_parent) {