### 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)

return animation_importer ? "AnimationLibrary" : "PackedScene";
}
int ResourceImporterScene::get_format_version() const {
	return 1;
}
bool ResourceImporterScene::get_option_visibility(const String &p_path, const String &p_option, const HashMap<StringName, Variant> &p_options) const {
	if (animation_importer) {
		if (p_option == "animation/import") { 
			return false;
		}
	} else if (p_option.begins_with("animation/")) {
		if (p_option != "animation/import" && !bool(p_options["animation/import"])) {
			return false;
		}
	}
	if (animation_importer && (p_option.begins_with("nodes/") || p_option.begins_with("meshes/") || p_option.begins_with("skins/"))) {
		return false; 
	}
	if (p_option == "meshes/lightmap_texel_size" && int(p_options["meshes/light_baking"]) != 2) {
		
		return false;
	}
	for (int i = 0; i < post_importer_plugins.size(); i++) {
		Variant ret = post_importer_plugins.write[i]->get_option_visibility(p_path, animation_importer, p_option, p_options);
		if (ret.get_type() == Variant::BOOL) {
			return ret;
		}
	}
	for (Ref<EditorSceneFormatImporter> importer : importers) {
		Variant ret = importer->get_option_visibility(p_path, animation_importer, p_option, p_options);