### 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_READ_THREAD_GUARD_V(Transform2D());
	Transform2D container_transform;
	SubViewportContainer *c = Object::cast_to<SubViewportContainer>(get_parent());
	if (c) {
		if (c->is_stretch_enabled()) {
			container_transform.scale(Vector2(c->get_stretch_shrink(), c->get_stretch_shrink()));
		}
		container_transform = c->get_viewport()->get_screen_transform_internal(p_absolute_position) * c->get_global_transform_with_canvas() * container_transform;
	} else {
		WARN_PRINT_ONCE("SubViewport is not a child of a SubViewportContainer. get_screen_transform doesn't return the actual screen position.");
	}
	return container_transform * get_final_transform();
}
Transform2D SubViewport::get_popup_base_transform() const {
	ERR_READ_THREAD_GUARD_V(Transform2D());
	if (is_embedding_subwindows()) {
		return Transform2D();
	}
	SubViewportContainer *c = Object::cast_to<SubViewportContainer>(get_parent());
	if (!c) {
		return get_final_transform();
	}
	Transform2D container_transform;
	if (c->is_stretch_enabled()) {
		container_transform.scale(Vector2(c->get_stretch_shrink(), c->get_stretch_shrink()));
	}
	return c->get_screen_transform() * container_transform * get_final_transform();
}
bool SubViewport::is_directly_attached_to_screen() const {