Figured it out by combing through the reference/reframing the problem.
In case it helps someone else –
Because SQLAlchemy ORM is based on an identity map model, one cannot map (or automap) a table that does not have a primary key. An arbitrary primary key should be specified.
http://docs.sqlalchemy.org/en/latest/faq/ormconfiguration.html#how-do-i-map-a-table-that-has-no-primary-key