Although, from the user's perspective of how the geometry is defined, it is the electrode
For definiteness, the system which ATK actually performs the calculation on, looks like
L-LP-C-RP-R (p for padding)
where C=central region and L/LP and R/RP are the left and right electrode geometries. During the self-consistent two-probe calculation, the real space quantities in L and R are fixed to their bulk values, while those in LP and RP are allowed to vary.
So, again, from the perspective of how the system is defined (names of variables etc), the system is L-C-R, and the real space density and effective potential vary freely across this region.