This is one of those cases where we are doing something to a hierarchy and it would be preferred to do this all in evaluated domain?
Seems like we need to do something similar to rB26d4a2a5169472369829905a960786390bc09c0e in object_origin_set_exec as well

Object *ob_eval = DEG_get_evaluated_object(depsgraph, ob);
BKE_object_transform_copy(ob_eval, ob);

BKE_object_where_is_calc(depsgraph, scene, ob_eval);
if (ob->type == OB_ARMATURE) {
  /* needed for bone parents */
  BKE_pose_where_is(depsgraph, scene, ob_eval);
}

but since that seems to be failing for nested relationships (see T66525) I think it makes sense if @Sergey Sharybin (sergey) squashes this nastyness for this report as well?
(@Sergey Sharybin (sergey): feel free to bounce back -- I just think you will kill it faster....)