### 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)

Control *over = gui_find_control(pos);
			if (over) {
				gui.touch_focus[touch_index] = over->get_instance_id();
				bool stopped = false;
				if (over->can_process()) {
					touch_event = touch_event->xformed_by(Transform2D()); 
					pos = over->get_global_transform_with_canvas().affine_inverse().xform(pos);
					touch_event->set_position(pos);
					stopped = _gui_call_input(over, touch_event);
				}
				if (stopped) {
					set_input_as_handled();
				}
				return;
			}
		} else {
			bool stopped = false;
			ObjectID control_id = gui.touch_focus[touch_index];
			Control *over = control_id.is_valid() ? Object::cast_to<Control>(ObjectDB::get_instance(control_id)) : nullptr;
			if (over && over->can_process()) {
				touch_event = touch_event->xformed_by(Transform2D()); 
				pos = over->get_global_transform_with_canvas().affine_inverse().xform(pos);
				touch_event->set_position(pos);
				stopped = _gui_call_input(over, touch_event);
			}
			if (stopped) {
				set_input_as_handled();
			}
			gui.touch_focus.erase(touch_index);
			return;