I would agree with the machinist if a .040 turn is needed. Probably tough to find bearings that size too. .010 or may be .020 is standard. .030 or more is a bit too much in my opinion. There's lots of cranks around. New and used.
FWIW.... even RockAuto lists .040" under size. But yes, lots of crank around to be had. I'd be more worried about the shop undercutting the shoulders' radius on the journals than turning down .040".