### Godot version

v4.2.dev.custom_build [60f3b7967]

### System information

Debian Linux X11 Xfce

### Issue description

Physics Picking within a `SubViewport` happens with `InputEventMouse` even when mouse events are disabled via `SubViewportContainer.mouse_filter = Control.MOUSE_FILTER_IGNORE`

The problem is that passive hovering still happens in the `SubViewport` with `SubViewportContainer.mouse_filter = Control.MOUSE_FILTER_IGNORE`.

I assume that it is a regression from #78017.

This was initially reported as a side-effect in #79271, which got closed, because the main issue was resolved.



### Steps to reproduce

1. Load and run MRP
2. move mouse over Icon

I would expect, that the `Area2D` receives no `InputEventMouse`, however it gets `_input_event` and also mouse-entered and mouse-exited signals.

### Minimal reproduction project

[IgnorePassiveHover.zip](https://github.com/godotengine/godot/files/12044510/IgnorePassiveHover.zip)

if (p_window == nullptr) {
		
		if (gui.subwindow_focused) {
			gui.subwindow_focused->_event_callback(DisplayServer::WINDOW_EVENT_FOCUS_OUT);
			gui.subwindow_focused = nullptr;
			gui.subwindow_drag = SUB_WINDOW_DRAG_DISABLED;
		}
		Window *this_window = Object::cast_to<Window>(this);
		if (this_window) {
			this_window->_event_callback(DisplayServer::WINDOW_EVENT_FOCUS_IN);
		}
		return;
	}
	int index = _sub_window_find(p_window);
	ERR_FAIL_COND(index == -1);
	if (p_window->get_flag(Window::FLAG_NO_FOCUS)) {
		
		if (gui.subwindow_focused) {
			gui.subwindow_focused->_event_callback(DisplayServer::WINDOW_EVENT_FOCUS_OUT);
			gui.subwindow_focused = nullptr;
			gui.subwindow_drag = SUB_WINDOW_DRAG_DISABLED;
		}
		
		SubWindow sw = gui.sub_windows[index];
		gui.sub_windows.remove_at(index);
		gui.sub_windows.push_back(sw);
		_sub_window_update_order();