SteveMann:
Since the overwhelming majority of Arduino boards are using the ATMega32U4, am I safe in thinking that I could default to the ATMega32U4 pin assignments prior to the tests for other boards?
Actually, I think you'll find that the overwhelming majority of Arduino boards use the '328P - that seems to be the gold standard. I believe that the '32U4 is only used in handful of boards.
But that aside, I think you are on the right track with your definition organization ideas.