The answer to the second question does say that, but then backpedals with the "In other words, the certificate holder elects not to conduct an IFR flight using the single pilot with a functioning autopilot option".

Difficult question, that letter does not really answer that question either.

Can you use both a functional autopilot AND a second-in-command, while having the SIC as a required crewmember.

I'd say if anyone asks FAA for a legal interpretation, you better word the question damn well so you won't get an answer you won't like.