### 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 (selecting) {
		return;
	}
	TreeItem *item = mesh_tree->get_selected();
	String type = item->get_meta("type");
	String import_id = item->get_meta("import_id");
	_select(mesh_tree, type, import_id);
}
void SceneImportSettings::_scene_tree_selected() {
	if (selecting) {
		return;
	}
	TreeItem *item = scene_tree->get_selected();
	String type = item->get_meta("type");
	String import_id = item->get_meta("import_id");
	_select(scene_tree, type, import_id);
}
void SceneImportSettings::_viewport_input(const Ref<InputEvent> &p_input) {
	float *rot_x = &cam_rot_x;
	float *rot_y = &cam_rot_y;
	float *zoom = &cam_zoom;
	if (selected_type == "Mesh" && mesh_map.has(selected_id)) {
		MeshData &md = mesh_map[selected_id];
		rot_x = &md.cam_rot_x;
		rot_y = &md.cam_rot_y;
		zoom = &md.cam_zoom;
	} else if (selected_type == "Material" && material_map.has(selected_id)) {
		MaterialData &md = material_map[selected_id];