### 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)

if (control) {
			if (control->data.mouse_filter != Control::MOUSE_FILTER_IGNORE) {
				control->_call_gui_input(ev);
			}
			if (!control->is_inside_tree() || control->is_set_as_top_level()) {
				break;
			}
			if (gui.key_event_accepted) {
				stopped = true;
				break;
			}
			if (control->data.mouse_filter == Control::MOUSE_FILTER_STOP && is_pointer_event && !(is_scroll_event && control->data.force_pass_scroll_events)) {
				
				stopped = true;
				break;
			}
		}
		if (is_input_handled()) {
			
			break;
		}
		if (ci->is_set_as_top_level()) {
			break;
		}
		ev = ev->xformed_by(ci->get_transform()); 
		ci = ci->get_parent_item();
	}
	return stopped;
}
void Viewport::_gui_call_notification(Control *p_control, int p_what) {