### 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)

scene_tree = memnew(Tree);
	scene_tree->set_name(TTR("Scene"));
	data_mode->add_child(scene_tree);
	scene_tree->connect("cell_selected", callable_mp(this, &SceneImportSettings::_scene_tree_selected));
	mesh_tree = memnew(Tree);
	mesh_tree->set_name(TTR("Meshes"));
	data_mode->add_child(mesh_tree);
	mesh_tree->set_hide_root(true);
	mesh_tree->connect("cell_selected", callable_mp(this, &SceneImportSettings::_mesh_tree_selected));
	material_tree = memnew(Tree);
	material_tree->set_name(TTR("Materials"));
	data_mode->add_child(material_tree);
	material_tree->connect("cell_selected", callable_mp(this, &SceneImportSettings::_material_tree_selected));
	material_tree->set_hide_root(true);
	SubViewportContainer *vp_container = memnew(SubViewportContainer);
	vp_container->set_h_size_flags(Control::SIZE_EXPAND_FILL);
	vp_container->set_custom_minimum_size(Size2(10, 10));
	vp_container->set_stretch(true);
	vp_container->connect("gui_input", callable_mp(this, &SceneImportSettings::_viewport_input));
	property_split->add_child(vp_container);
	base_viewport = memnew(SubViewport);
	vp_container->add_child(base_viewport);
	base_viewport->set_use_own_world_3d(true);
	camera = memnew(Camera3D);
	base_viewport->add_child(camera);
	camera->make_current();
	if (GLOBAL_GET("rendering/lights_and_shadows/use_physical_light_units")) {
		camera_attributes.instantiate();
		camera->set_attributes(camera_attributes);
	}