Is it anything like how Cape Air operates? I saw you posted in that FO thread, and I addressed it there but I don't mind saying it again.

Cape Air is required to have two-person crews. However, we have a waiver saying that we can use an autopilot in lieu of an actual FO. On two-pilot flights, even with a functional autopilot, we do NOT excersise that waiver, making the FO a required crew member. Just because we CAN use that waiver doesn't mean we MUST use it. We are not required to use the autopilot instead of a FO, even if it's working, but we CAN. We just don't when we have a FO. We choose when to exercise the waiver.

That's why Cape Air FOs can log time on any flight they fly, working autopilot or not. Again, it's an optional WAIVER, not a requirement.

So, if your company operates under the same principles that we do, that's how I'd present it.