### 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)

List<ObjectID> to_erase;
	for (const KeyValue<ObjectID, uint64_t> &E : physics_2d_mouseover) {
		if (!p_clean_all_frames && E.value == p_frame_reference) {
			continue;
		}
		Object *o = ObjectDB::get_instance(E.key);
		if (o) {
			CollisionObject2D *co = Object::cast_to<CollisionObject2D>(o);
			if (co && co->is_inside_tree()) {
				if (p_clean_all_frames && p_paused_only && co->can_process()) {
					continue;
				}
				co->_mouse_exit();
			}
		}
		to_erase.push_back(E.key);
	}
	while (to_erase.size()) {
		physics_2d_mouseover.erase(to_erase.front()->get());
		to_erase.pop_front();
	}
	
	List<Pair<ObjectID, int>> shapes_to_erase;
	for (KeyValue<Pair<ObjectID, int>, uint64_t> &E : physics_2d_shape_mouseover) {
		if (!p_clean_all_frames && E.value == p_frame_reference) {
			continue;
		}
		Object *o = ObjectDB::get_instance(E.key.first);
		if (o) {
			CollisionObject2D *co = Object::cast_to<CollisionObject2D>(o);