### 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)

selecting = true;
	scene_import_settings_data->hide_options = false;
	if (p_type == "Node") {
		node_selected->hide(); 
		mesh_preview->hide();
		if (Object::cast_to<Node3D>(scene)) {
			Object::cast_to<Node3D>(scene)->show();
		}
		
		material_tree->deselect_all();
		mesh_tree->deselect_all();
		NodeData &nd = node_map[p_id];
		MeshInstance3D *mi = Object::cast_to<MeshInstance3D>(nd.node);
		if (mi) {
			Ref<Mesh> base_mesh = mi->get_mesh();
			if (base_mesh.is_valid()) {
				AABB aabb = base_mesh->get_aabb();
				Transform3D aabb_xf;
				aabb_xf.basis.scale(aabb.size);
				aabb_xf.origin = aabb.position;
				aabb_xf = mi->get_global_transform() * aabb_xf;
				node_selected->set_transform(aabb_xf);
				node_selected->show();
			}
		}
		if (nd.node == scene) {
			scene_import_settings_data->settings = &defaults;
			scene_import_settings_data->category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MAX;
		} else {