"Also, when you have the closed loop performance wrapped around it that also can alter what you measure (so why it's best to run autotune with default settings)"
I wasn't aware I was supposed to run autotune with default settings. So to clarify, you mean that modules altitude hold, vtol path follower, and maybe GPS should not be selected in the GCS when using the autotune module?
It just occurred to me I might be asking the wrong question. So far I've be doing autotune with "leveling" flight mode switched active.
Is that OK? I don't fly in rate mode, and don't even think I could keep the quad under control in rate mode while it's doing it's shaky thing during autotune.