While not your issue, InSpectre only takes a minute. I am highly interested if turning off the mitigations gives a big speed boost or not, for transcoding. Some tasks can be 25% or more faster. If you can compare the apples to apples that is.
You are experienced, but I’ll throw out some thoughts anyways. Does not seem like dirty power. Is the board needing a repasting/pads maybe? Temps all look good, especially for VRMs? Heavy load causing throttling already eliminated as possibility?