### 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)

String import_id;
	if (p_node->has_meta("import_id")) {
		import_id = p_node->get_meta("import_id");
	} else {
		import_id = "PATH:" + String(scene->get_path_to(p_node));
		p_node->set_meta("import_id", import_id);
	}
	ImporterMeshInstance3D *src_mesh_node = Object::cast_to<ImporterMeshInstance3D>(p_node);
	if (src_mesh_node) {
		MeshInstance3D *mesh_node = memnew(MeshInstance3D);
		mesh_node->set_name(src_mesh_node->get_name());
		mesh_node->set_transform(src_mesh_node->get_transform());
		mesh_node->set_skin(src_mesh_node->get_skin());
		mesh_node->set_skeleton_path(src_mesh_node->get_skeleton_path());
		if (src_mesh_node->get_mesh().is_valid()) {
			Ref<ImporterMesh> editor_mesh = src_mesh_node->get_mesh();
			mesh_node->set_mesh(editor_mesh->get_mesh());
		}
		p_node->replace_by(mesh_node);
		memdelete(p_node);
		p_node = mesh_node;
	}
	String type = p_node->get_class();
	if (!has_theme_icon(type, SNAME("EditorIcons"))) {
		type = "Node3D";
	}
	Ref<Texture2D> icon = get_theme_icon(type, SNAME("EditorIcons"));
	TreeItem *item = scene_tree->create_item(p_parent_item);
	item->set_text(0, p_node->get_name());
	if (p_node == scene) {