I think the cases I am presenting are actually one-to-many relations but they involve nesting of entities that have multiple parent types.
This is not exactly true. In my case, an entity can have parents of different types but those are one-to-many relations.
For example a person works for a company but can also be part of a department within than company. When I create a hierarchy of organization → organizational unit (department) → contact, Fibery gets confused on where to position the contact: under the organization or the department.
I described a possible solution in this post, basically suggesting to work from the deepest level of the hierarchy upwards to find the first “parent” for the entity.
Now when many-to-many relations are involved, I think the above process could simply be ignored so that the same entity appears multiple times in the hierarchy.
I think the approach that I am suggesting above will also address the same-type reference issues at deeper levels of the hierarchy as well. Those situations are generally one-to-many relations between the child and parent nodes.
Apologies if this still doesn’t make sense. It is a rather interesting and challenging issue. If it helps, I can try and describe it to you in a short screen capture or a short zoom call.