I should say that this is really good to do at the begining

,
just to make sure you have all setup right (!) and can explain "ghost currents" if you have them
What I do is run model similar like you but with analitical (for my region specific) vertical T & S; just to be sure that there are no horizontal gradient introduced in the initial phase. Than after some time (depending on the grid/region), say 2 weeks, you could notice that you have growing velocities at the bottom. This should represent mayor contribution from HPGE (Horizontal Pressure Gradient Error) because of imperfect vertical coordinate. Those regions with higher bottom velocities should correspond with regions characterised with higher values of rx1 -> (in a fact you can compute it and plot it)
If this is not acceptable for you reconsider to smooth bahtymetry more or change vertical structure (less vertical levels, higher theta_s ...)
Cheers
Ivica