When applying brakes, what slows you down is friction and friction builds heat and that heat transfers in to the rotor and the vent fins in the rotor helps dissipate that heat while they are spinning. Over time the rotor will warp and also get grit imbedded in the surface of the rotor. To make sure the new pads have a clean smooth surface to "seat" in to, the shops will machine the surfaces of the rotor. The thing is, federal mpg mandates have caused the vehicle manufacturers to cut weight anywhere they can. Rotors are one of those places. Thinner means less weight. The new rotor starts out thinner and then to machine them can cause the thickness to get too close to minimum thickness spec or under that spec. That means the rotor will not dissipate heat as well and will warp quicker and cause brake pedal pulsation that you feel in your foot and in extreme cases, causes a front end or even rear end shake. Over the years I have machined rotors on all types of rigs and even drums. I have also machined rotors with them still mounted on the hub and that is a whole other experience to set up and deal with.
IMO, replace with new rotors at every brake job. Use the cost of what the machining would be to go to help pay for new rotors. A Stealership may say, "we don't credit back machining fees if you buy new rotors". Hence the name Stealership.
