### 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)

int index = _sub_window_find(p_window);
	ERR_FAIL_COND(index == -1);
	ERR_FAIL_NULL(RenderingServer::get_singleton());
	RS::get_singleton()->free(gui.sub_windows[index].canvas_item);
	gui.sub_windows.remove_at(index);
	if (gui.sub_windows.size() == 0) {
		RS::get_singleton()->free(subwindow_canvas);
		subwindow_canvas = RID();
	}
	if (gui.currently_dragged_subwindow == p_window) {
		gui.subwindow_drag = SUB_WINDOW_DRAG_DISABLED;
		gui.currently_dragged_subwindow = nullptr;
	}
	if (gui.subwindow_focused == p_window) {
		Window *new_focused_window;
		Window *parent_visible = p_window->get_parent_visible_window();
		gui.subwindow_focused->_event_callback(DisplayServer::WINDOW_EVENT_FOCUS_OUT);
		if (parent_visible) {
			new_focused_window = parent_visible;
		} else {
			new_focused_window = Object::cast_to<Window>(this);
		}
		if (new_focused_window) {
			int new_focused_index = _sub_window_find(new_focused_window);
			if (new_focused_index != -1) {
				gui.subwindow_focused = new_focused_window;
			} else {
				gui.subwindow_focused = nullptr;
			}
			new_focused_window->_event_callback(DisplayServer::WINDOW_EVENT_FOCUS_IN);