I did a bit of googling. Evidently (and I hadn't realised this) for most DSLRs in live view (and presumably mirrorless), AF is done with the lens at the aperture it will be exposed at, not wide open as with phase detect. So you are right that focus shift is not an issue for mirrorless cameras (or DSLRs in live view).
I suppose what I don't get is why DSLRs in phase detect AF don't use the actual aperture (instead of wide open) when the lens is set at, say, f/2.8 or wider. Clearly f/2.8 is plenty of light for phase detect to be effective. And that would virtually eliminate focus shift issues.













