it really makes little difference whether the holes are drilled prior to or subsequent to the heat treatment operation. from a manfacturing standpoint there are arguements for both positions.
personally, i would locate and drill the trunnion/stock latch holes/rear receiver profile prior to heat treatment. although the steel is still machineable after heat treatment, i prefer to remove material when it's easiest to do so.
also, due to the minimal material (and its' location/shape) removal prior to heat treatment, distortion should be next to zero.
ask chris (at ak-usa) what his opinion is, but i see no concern for either approach.