Is it correct that both the Generic Contact policy and the Offer Optimization Rules only apply to the Program Run output and will ignore any subsequent outbound messages that might emanate from any in flight offer flow?
It is correct. They won't apply to subsequent messages emanting from the offer flow.
A note on 'Generic Contact Policy': There is no such thing as a 'Generic Contact Policy'. It's just an artefact made available to students in the exercise system. You will not find it in NBAM out-of-the-box.