It's the Raynox teleconverter. It is somehow "decalibrating" the focus-assist magnification. The odd thing is that, as I'm sure you can attest based on your great 2020 shots, the autofucus is dead on. If I remove the Raynox, what I see in focus assist is what I get on the memory card. With the converter, everything looks perfect in the viewfinder, and then out of focus in the result, evident even in the 1 second review in the evf. Even in full manual mode.
When I use your technique, half-press while focusing, the shots come out in focus. So I scratched my head. You had said to turn off assist when doing this. On my camera, in manual mode, if I hold the shutter half way while turning the focus ring, assist is automatically disabled, regardless of menu setting. So, just for kicks, I turned off assist in the menu. With assist disabled, manually focusing yields shots that are consistent with the evf focus, regardless of shutter position, hence my conclusion that focus assist is the real culprit when combined with the 2020. I say this because without the converter, I can use assist in manual focus and achieve results equal to or better than auto (on a really good day :G).
What we need is folks with other tele converters, _especially_ the panasonic, to try this & post results. If the phenomenon exists w/ the Panasonic converter, I guess we have a bug. Either way, I'm contacting Raynox. I don't think this should be happening. One thing that I'd like to try, but I don't have the hardware, is to stack a few adapters, etc to move the lens out a bit & see if I can get assist back into focus. Vignetting at less than max zoom is not an issue for me.