### Godot version

v4.1.stable.official [970459615]

### System information

Godot v4.1.stable - Windows 10.0.22621 - Vulkan (Forward+) - dedicated NVIDIA GeForce GTX 1660 Ti (NVIDIA; 31.0.15.3598) - AMD Ryzen 7 3700X 8-Core Processor (16 Threads)

### Issue description

is_input_handled() is returning True, even though set_input_as_handled() has not been called.

Example:
`func _input_event(viewport, event, shape_idx):
	print(viewport.is_input_handled())`

Returns 'True', should return 'False'

### Steps to reproduce

1. Create a new project and add a Node2D as the root
2. Add a child Area2D node containing a CollisionShape2D and a Sprite2D
3. Either create the _input_event(viewport, event, shape_idx) or connect _on_input_event(viewport, event, shape_idx)
4. Print viewport.is_input_handled()
5. True is printed.

### Minimal reproduction project

[input_test.zip](https://github.com/godotengine/godot/files/12063748/input_test.zip)

ERR_READ_THREAD_GUARD_V(Transform2D());
	Transform2D container_transform;
	SubViewportContainer *c = Object::cast_to<SubViewportContainer>(get_parent());
	if (c) {
		if (c->is_stretch_enabled()) {
			container_transform.scale(Vector2(c->get_stretch_shrink(), c->get_stretch_shrink()));
		}
		container_transform = c->get_viewport()->get_screen_transform_internal(p_absolute_position) * c->get_global_transform_with_canvas() * container_transform;
	} else {
		WARN_PRINT_ONCE("SubViewport is not a child of a SubViewportContainer. get_screen_transform doesn't return the actual screen position.");
	}
	return container_transform * get_final_transform();
}
Transform2D SubViewport::get_popup_base_transform() const {
	ERR_READ_THREAD_GUARD_V(Transform2D());
	if (is_embedding_subwindows()) {
		return Transform2D();
	}
	SubViewportContainer *c = Object::cast_to<SubViewportContainer>(get_parent());
	if (!c) {
		return get_final_transform();
	}
	Transform2D container_transform;
	if (c->is_stretch_enabled()) {
		container_transform.scale(Vector2(c->get_stretch_shrink(), c->get_stretch_shrink()));
	}
	return c->get_screen_transform() * container_transform * get_final_transform();
}
bool SubViewport::is_directly_attached_to_screen() const {