I don't think peteeng would be using many screws for his Robot build, they do use a lot of Belt drives though.
Both motors are getting the same signal, so both should be out, by the same amount, unless one side was over loaded, they could still each be Homed using a separate switch, I don't think this would be a good idea though, some do this thing called Gantry squaring, ( 2 ) switches, if you can square your Gantry by Homing you have a structural problem with your machine, and this will always be a problem if you have to use Gantry squaring
I don't use Steppers and never will, with a Ac servo you can use the encoder Z pulse / Index pulse, which will give you the same perfect Home position every time, once you establish the Encoder Z pulse, on both motors you can then mount or clamp the Ballscrew mount in place.
The same should apply to setup your Steppers, but lost steps are lost steps, which could happen if one side of you Gantry was over loaded, this does not happen with Ac servos they don't loose steps, ( 1 ) output may not work for you, if you need independents of each screw, another way would be to use ( 1 ) motor and a belt drive to the 2 screws, if your Gantry is not very wide then this would be better than using ( 2 ) motors.