Nope, its the stem height.
Did this so called machinist even tell you the current installed stem height???
That is the biggest crock I have ever heard, and the detail of the machinist talking about honing the rocker saddles without doing a sweep test by simply dropping the valve down the measly .020 or so thousanths and open closing the valve with the rocker dye tells me someone needs a new machinist.
Oh well, enjoy your mopar.