1. This is the be expected, given the concept of "electrode copy" in the central region. What you need to do is either constrain the "electrode copy" during the relaxation, or relax the system as a two-probe geometry.
2. You set the parameters of the method as usual, when you set up the device calculation (as if it was already relaxed).
3. It's faster because you are not running a two-probe calculation (no electrodes, no open boundary conditions). The results are very similar, but not identical.
However, you can do something different, there is a trick
If you set up the device calculation to be
non-selfconsistent, ATK will automatically do the central region optimization as bulk, while imposing the relevant constraints. This is generally the best option.