### 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)

ERR_FAIL_COND_MSG(current_option_list == nullptr, "add_import_option() can only be called from get_import_options()");
	add_import_option_advanced(p_default_value.get_type(), p_name, p_default_value);
}
void EditorScenePostImportPlugin::add_import_option_advanced(Variant::Type p_type, const String &p_name, Variant p_default_value, PropertyHint p_hint, const String &p_hint_string, int p_usage_flags) {
	ERR_FAIL_COND_MSG(current_option_list == nullptr, "add_import_option_advanced() can only be called from get_import_options()");
	current_option_list->push_back(ResourceImporter::ImportOption(PropertyInfo(p_type, p_name, p_hint, p_hint_string, p_usage_flags), p_default_value));
}
void EditorScenePostImportPlugin::get_internal_import_options(InternalImportCategory p_category, List<ResourceImporter::ImportOption> *r_options) {
	current_option_list = r_options;
	GDVIRTUAL_CALL(_get_internal_import_options, p_category);
	current_option_list = nullptr;
}
Variant EditorScenePostImportPlugin::get_internal_option_visibility(InternalImportCategory p_category, bool p_for_animation, const String &p_option, const HashMap<StringName, Variant> &p_options) const {
	current_options = &p_options;
	Variant ret;
	GDVIRTUAL_CALL(_get_internal_option_visibility, p_category, p_for_animation, p_option, ret);
	current_options = nullptr;
	return ret;
}
Variant EditorScenePostImportPlugin::get_internal_option_update_view_required(InternalImportCategory p_category, const String &p_option, const HashMap<StringName, Variant> &p_options) const {