### 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)

MeshData &md = mesh_map[p_id];
		if (md.mesh_node != nullptr) {
			if (p_from != mesh_tree) {
				md.mesh_node->uncollapse_tree();
				md.mesh_node->select(0);
				mesh_tree->ensure_cursor_is_visible();
			}
			if (p_from != scene_tree) {
				md.scene_node->uncollapse_tree();
				md.scene_node->select(0);
				scene_tree->ensure_cursor_is_visible();
			}
		}
		mesh_preview->set_mesh(md.mesh);
		mesh_preview->show();
		material_tree->deselect_all();
		scene_import_settings_data->settings = &md.settings;
		scene_import_settings_data->category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MESH;
	} else if (p_type == "Material") {
		node_selected->hide();
		if (Object::cast_to<Node3D>(scene)) {
			Object::cast_to<Node3D>(scene)->hide();
		}
		mesh_preview->show();
		MaterialData &md = material_map[p_id];
		material_preview->set_material(md.material);
		mesh_preview->set_mesh(material_preview);
		if (p_from != mesh_tree) {
			md.mesh_node->uncollapse_tree();
			md.mesh_node->select(0);