Honestly I am not sure what happens with joints as child entities. When baking this doesn’t happen unless I am mistaken.
Maybe because they are children of a dynamic entity, they automatically also obtain transformation components, but that would surprise me when runtime created.
The transforms on joint entities are not considered. So moving them or not makes no difference.
As to where to do your transformation or instantiation, I suggest the AfterPhysicsSystemGroup. That’s a safe moment for pretty much anything physics related. Alternatively, the BeforePhysicsSystemGroup would work as well I think.