How to retain visual breadcrumbs w/ tricky URL structure? Custom post template?

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If I understand description and discussion correctly the issue seems to be using pages as nodes in structure. This is somewhat confusing since page are content entity, not structural.

I agree with suggestion that it would make sense to use taxonomies (custom or native categories) instead. That will give you:

  1. Clear hierarchical structure of content.

  2. Option to use it in links to make them more visual.

  3. Easier to handle structure for breadcrumbs.

  4. Convenient way to tweak looks and such with respective templates.