### 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 = p_node->get_meta("import_id", "PATH:" + p_root->get_path_to(p_node));
	Dictionary node_settings;
	if (p_node_data.has(import_id)) {
		node_settings = p_node_data[import_id];
	}
	{
		
		node_settings = node_settings.duplicate(true);
		
		List<ImportOption> iopts;
		get_internal_import_options(INTERNAL_IMPORT_CATEGORY_ANIMATION_NODE, &iopts);
		for (const ImportOption &E : iopts) {
			if (!node_settings.has(E.option.name)) {
				node_settings[E.option.name] = E.default_value;
			}
		}
	}
	if (Object::cast_to<AnimationPlayer>(p_node)) {
		AnimationPlayer *ap = Object::cast_to<AnimationPlayer>(p_node);
		List<StringName> anims;
		ap->get_animation_list(&anims);
		for (const StringName &name : anims) {
			Ref<Animation> anim = ap->get_animation(name);
			Array animation_slices;
			if (p_animation_data.has(name)) {
				Dictionary anim_settings = p_animation_data[name];
				int slices_count = anim_settings["slices/amount"];
				for (int i = 0; i < slices_count; i++) {
					String slice_name = anim_settings["slice_" + itos(i + 1) + "/name"];
					int from_frame = anim_settings["slice_" + itos(i + 1) + "/start_frame"];