Well say he takes 0.100" off the deck any head upgrade down the line will need to be mill for the intake to fit, now you got an intake or head that only work's will blocks that been milled a 0.100". If you go through a bunch of upgrades could leave a lot of one off parts.
Plus your building power on stock pistons limiting future upgrade power capablies valve clearance etc..
Even so if it's just for intake, why would you rather a 0.100" milled stock piston block vs a block with decent aftermarket pistons and a cleanup mill job?