Duplicated classes and methods in Sphinx API docs

[garrison]

What is the expected enhancement?

Currently, there is a build of the API reference at https://qiskit-community.github.io/prototype-qrao/apidocs/. However, the use of Sphinx could be improved. Most notably, some classes and functions are duplicated, e.g. on the encoding page. The duplication is presumably because those identifiers are included explicitly in the autosummary directive; however, if identifiers aren't included there, they end up not being clickable for additional detail (e.g., as is currently the case with EncodingCommutationVerifier). I've not been able to figure out Sphinx sufficiently to fix this.