I've got a fix for the lsst.daf.butler.Config API reference issue.
The problem is here: https://github.com/astropy/sphinx-automodapi/blob/6c3960abd26e169a83eb54592a9820a2d7e3b667/sphinx_automodapi/automodsumm.py#L549-L557
First, my mistake was that I didn't set automodsumm_inherited_members = True in the Sphinx config. I'm doing this now, and as a benefit, we actually get inherited members now in our docs.
The consequence of accidentally disabling documenting inherited members before is that if a class has a _slots attribute, it looks for members only in slots and doesn't use dir(). I think the MutableMapping base class adds these slots, but in this case, the logic in automodsumm isn't appropriate since it means that effectively _none of the class's own members are discovered and documented.
Thus the overall solution for us is to use automodsumm_inherited_members = True in our Sphinx configurations through Documenteer.