Addendum -
There are 2 separate issues here after further exploring it.
1 ) When adding a new reference collection at the root level of a category, it will add a default entry. If you remove that default entry, you can no longer edit the reference category in the collection edit interface, and your only able to add blank references on items inside a category. IF you add the default reference back you can then edit the reference category.
This is a minor issue, though as a quality of life improvement I'd like to be able to have a default reference type set for a collection without requiring it to actually have an entry, since an empty collection is still valid. I'm able to work around this by removing the default reference inside each individual item.
2 ) I do think this falls down when references are nested. So if I have a reference category pointing to a thing that also has a reference collection inside of it, it will never correctly assign itself to the proper category. So I definitely would like the developer to look into this if he can.
It's also possible it's failing silently somewhere ( Like a broken record somewhere ), but in either case I'm not getting expected behavior.
For the moment I won't be using nested references and I'll just build the intervening layer in code on game boot up and store the raw data flat, but it's a bit of a hacky approach I'd like to avoid.