### 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 (over) {
			bool stopped = false;
			if (over->can_process()) {
				Transform2D localizer = over->get_global_transform_with_canvas().affine_inverse();
				Size2 pos = localizer.xform(drag_event->get_position());
				Vector2 velocity = localizer.basis_xform(drag_event->get_velocity());
				Vector2 rel = localizer.basis_xform(drag_event->get_relative());
				drag_event = drag_event->xformed_by(Transform2D()); 
				drag_event->set_velocity(velocity);
				drag_event->set_relative(rel);
				drag_event->set_position(pos);
				stopped = _gui_call_input(over, drag_event);
			}
			if (stopped) {
				set_input_as_handled();
			}
			return;
		}
	}
	if (mm.is_null() && mb.is_null() && p_event->is_action_type()) {
		if (gui.dragging && p_event->is_action_pressed("ui_cancel") && Input::get_singleton()->is_action_just_pressed("ui_cancel")) {
			_perform_drop();
			set_input_as_handled();
			return;
		}
		if (gui.key_focus && !gui.key_focus->is_visible_in_tree()) {
			gui.key_focus->release_focus();
		}
		if (gui.key_focus) {
			gui.key_event_accepted = false;