### 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)

_cleanup_mouseover_colliders(true, p_paused_only);
#ifndef _3D_DISABLED
	if (physics_object_over.is_valid()) {
		CollisionObject3D *co = Object::cast_to<CollisionObject3D>(ObjectDB::get_instance(physics_object_over));
		if (co) {
			if (!co->is_inside_tree()) {
				physics_object_over = ObjectID();
				physics_object_capture = ObjectID();
			} else if (!(p_paused_only && co->can_process())) {
				co->_mouse_exit();
				physics_object_over = ObjectID();
				physics_object_capture = ObjectID();
			}
		}
	}
#endif 
}
void Viewport::_cleanup_mouseover_colliders(bool p_clean_all_frames, bool p_paused_only, uint64_t p_frame_reference) {