The "right" answer is what is spelled out in the regs:
135.101
Except as provided in Sec. 135.105, no person may operate an aircraft carrying passengers under IFR unless there is a second in command in the aircraft.
135.105
(a) . . .a person may operate an aircraft without a second in command, if it is equipped with an operative approved autopilot system and the use of that system is authorized by appropriate operations specifications.
(b) The certificate holder may apply for an amendment of its operations specifications to authorize the use of an autopilot system in place of a second in command.
There it is. There's no need to get the FSDO involved. It's 100% legit. Sure, you MAY operate with an autopilot instead of an SIC... but you don't NEED to. There's no requirement there, it doesn't say "a person SHALL operate an aircraft without a second in command, if it is equipped with an operative approved autopilot system" or "a person MUST operate an aircraft without a second in command, if it is equipped with an operative approved autopilot system." Yes, it says IFR, but I did all my 135 flights on IFR flight plans (it's so much easier that way!), so that part didn't matter to me and my FOs. HOWEVER: If your company's Op Specs specifically state that an SIC is required for all flights, IFR or VFR, then that becomes ruling and you're able to log SIC even on VFR flights. Cape Air's Op Specs don't say that, but maybe yours do.
Moving on... You're not REQUIRED to use the autopilot in lieu of an SIC, but you can if you want. You can choose NOT to use the autopilot in lieu of an SIC, and that's why you can log SIC time. If you're NOT using the autopilot in lieu of an SIC, then the SIC is a required crewmember.
There's no semantics about it, Rick, it's right there in gray and gray :). BTW, where are the smilies? I'd have put one there...
Anyway, there's no need to convince a FSDO. The time is 100% loggable towards your ATP. It's legitimate SIC time per 135.101. Granted, the powers that be at the new company CAN pick and choose what time they like and what time they don't like.
For example, some airlines only count PIC time as time when you actually signed for the aircraft, so your part 91 legs wouldn't count as PIC as far as they're concerned. Yes, you were sole manipulator, but you didn't sign for the plane. It's still legal PIC per the FARs, and you still log it.