### 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)

gui.mouse_focus_mask.set_flag(mouse_button_to_mask(mb->get_button_index()));
				if (mb->get_button_index() == MouseButton::LEFT) {
					gui.drag_accum = Vector2();
					gui.drag_attempted = false;
				}
			}
			DEV_ASSERT(gui.mouse_focus);
			mb = mb->xformed_by(Transform2D()); 
			Point2 pos = gui.mouse_focus->get_global_transform_with_canvas().affine_inverse().xform(mpos);
			mb->set_position(pos);
#ifdef DEBUG_ENABLED
			if (EngineDebugger::get_singleton()) {
				Array arr;
				arr.push_back(gui.mouse_focus->get_path());
				arr.push_back(gui.mouse_focus->get_class());
				EngineDebugger::get_singleton()->send_message("scene:click_ctrl", arr);
			}
#endif
			if (mb->get_button_index() == MouseButton::LEFT) { 
				CanvasItem *ci = gui.mouse_focus;
				while (ci) {
					Control *control = Object::cast_to<Control>(ci);
					if (control) {
						if (control->get_focus_mode() != Control::FOCUS_NONE) {
							if (control != gui.key_focus) {
								control->grab_focus();
							}
							break;
						}
						if (control->data.mouse_filter == Control::MOUSE_FILTER_STOP) {