Rotors are made a bit wavy (I forget the amount but its in the .005ish range if I remember right) to "force" the pads away from the rotor to reduce friction. If the rotor was 100% parallel and flat the pads would always slightly drag on the rotor, the bit of wave pushes the pad off a few thousands, and you never feel it in the pedal.
It is tough to convince your mind that it is OK, but if you have the parts, it doenst take long to swap the hubs over if they do shake. I would put those on, take it for a drive, and if it pedal pulses you have maybe half an hour per side to remove the wheel, rotor and caliper, swap the hub, and put it back together. I would do that just to confirm that .011" face runout is or isnt OK.