### 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)

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);