It was about reversion. During overlap, exh gas 'reverses' direction & tries to enter the intake system, which is bad. Having some very slight port overhang disrupts this, without unduly affecting the incoming intake flow.
I have seen zero proof that making the manifold mismatch the head doing anything.
This came about because some shop in Arizona was doing big block Chevy’s with square port heads and oval port intakes. And it worked in that specific application.
It’s not universal. In fact DV is the only one I know still leg jumping that nonsense.
Several years ago Darin Morgan was on Drag Boss Garage and I specifically asked him this very question.
The short answer is it worked I that limited application but in almost all cases it doesn’t work.
If you are going to do the work to port the intake manifold make the ports match.
Especially on engines where the heads are the cork.
And IIRC that Chevy deal was some marine application.