### 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)

first_aabb = false;
		} else {
			contents_aabb.merge_with(aabb);
		}
	}
}
void SceneImportSettings::_update_scene() {
	scene_tree->clear();
	material_tree->clear();
	mesh_tree->clear();
	
	material_tree->create_item();
	mesh_tree->create_item();
	_fill_scene(scene, nullptr);
}
void SceneImportSettings::_update_view_gizmos() {
	if (!is_visible()) {
		return;
	}
	for (const KeyValue<String, NodeData> &e : node_map) {
		bool generate_collider = false;
		if (e.value.settings.has(SNAME("generate/physics"))) {
			generate_collider = e.value.settings[SNAME("generate/physics")];
		}
		MeshInstance3D *mesh_node = Object::cast_to<MeshInstance3D>(e.value.node);
		if (mesh_node == nullptr || mesh_node->get_mesh().is_null()) {
			
			continue;
		}
		TypedArray<Node> descendants = mesh_node->find_children("collider_view", "MeshInstance3D");