### 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)

GDCLASS(SceneImportSettingsData, Object)
	friend class SceneImportSettings;
	HashMap<StringName, Variant> *settings = nullptr;
	HashMap<StringName, Variant> current;
	HashMap<StringName, Variant> defaults;
	List<ResourceImporter::ImportOption> options;
	bool hide_options = false;
	String path;
	ResourceImporterScene::InternalImportCategory category = ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MAX;
	bool _set(const StringName &p_name, const Variant &p_value) {
		if (settings) {
			if (defaults.has(p_name) && defaults[p_name] == p_value) {
				settings->erase(p_name);
			} else {
				(*settings)[p_name] = p_value;
			}
			current[p_name] = p_value;
			if (SceneImportSettings::get_singleton()->is_editing_animation()) {
				if (category == ResourceImporterScene::INTERNAL_IMPORT_CATEGORY_MAX) {
					if (ResourceImporterScene::get_animation_singleton()->get_option_visibility(path, p_name, current)) {
						SceneImportSettings::get_singleton()->update_view();
					}
				} else {
					if (ResourceImporterScene::get_animation_singleton()->get_internal_option_update_view_required(category, p_name, current)) {
						SceneImportSettings::get_singleton()->update_view();
					}