### 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)

Vector3 center = camera_aabb.get_center();
	float camera_size = camera_aabb.get_longest_axis_size();
	camera->set_orthogonal(camera_size * zoom, 0.0001, camera_size * 2);
	Transform3D xf;
	xf.basis = Basis(Vector3(1, 0, 0), rot_x) * Basis(Vector3(0, 1, 0), rot_y);
	xf.origin = center;
	xf.translate_local(0, 0, camera_size);
	camera->set_transform(xf);
}
void SceneImportSettings::_load_default_subresource_settings(HashMap<StringName, Variant> &settings, const String &p_type, const String &p_import_id, ResourceImporterScene::InternalImportCategory p_category) {
	if (base_subresource_settings.has(p_type)) {
		Dictionary d = base_subresource_settings[p_type];
		if (d.has(p_import_id)) {
			d = d[p_import_id];
			List<ResourceImporterScene::ImportOption> options;
			if (editing_animation) {
				ResourceImporterScene::get_animation_singleton()->get_internal_import_options(p_category, &options);
			} else {
				ResourceImporterScene::get_scene_singleton()->get_internal_import_options(p_category, &options);
			}
			for (const ResourceImporterScene::ImportOption &E : options) {
				String key = E.option.name;
				if (d.has(key)) {
					settings[key] = d[key];
				}
			}
		}
	}
}
void SceneImportSettings::update_view() {