### 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)

ERR_MAIN_THREAD_GUARD;
	Transform2D xform = get_screen_transform_internal();
	Vector2 gpos = xform.xform(p_position);
	Input::get_singleton()->warp_mouse(gpos);
}
void Viewport::_gui_sort_roots() {
	if (!gui.roots_order_dirty) {
		return;
	}
	gui.roots.sort_custom<Control::CComparator>();
	gui.roots_order_dirty = false;
}
void Viewport::_gui_cancel_tooltip() {
	gui.tooltip_control = nullptr;
	if (gui.tooltip_timer.is_valid()) {
		gui.tooltip_timer->release_connections();
		gui.tooltip_timer = Ref<SceneTreeTimer>();
	}
	if (gui.tooltip_popup) {
		gui.tooltip_popup->queue_free();
	}
}
String Viewport::_gui_get_tooltip(Control *p_control, const Vector2 &p_pos, Control **r_tooltip_owner) {