This doesn't make a lot of sense off the bat, are there more details to the story that explain how CPU branch prediction performance depends on Windows behaviour somehow?
Basically (according to him) they disabled the spectre/meltdown mitigation if you were an admin - because you were an admin and have full rights to the machine anyway. So now they are doing that for all users?
He wasn't clear - or at least it wasn't clear to me. So the mitigations are no longer needed? I think I have more questions than before after listening to that.
Linux has different performance schedulers you can choose that can dramatically change performance dependant on workloads. It's very possible the CPU is being too smart for its own good and the way Windows is lining stuff up it's not executing branches or something like that.
This is just shooting from the hip, but there is a ton of different stuff going on in both the OS and the CPU around this.
The mitigations for Spectre/Meltdown involved deliberately breaking branch prediction across the user/kernel boundary, so it may be as simple as them disabling some mitigations which turned out to not be needed anymore on newer CPU architectures.