You might have some small deflection because of the residual anti-skate, but I'd venture that it won't be much. One way to check is to look on from the front to see whether the cantilever visibly deflects when the stylus contacts the protractor surface. If not, don't worry about it. If you see a little deflection, you can try rotating the cartridge to offset it. You could try listening both ways to see if you hear a difference.
Aligning cart on Rega style arms without defeatable anti-skating?
Rega arms use a magnetic adjustment to apply anti-skate force. It is my understanding that many (most?) Rega arms cannot have their anti-skating completely disabled due to this since at the zero setting, the magnet may not be far enough away to completely be ineffective. This probably varies with manufacturing tolerances.
In my experience, zero anti-skate setting always has a small amount of lateral force applied which is most obvious when trying to balance the tonearm. After applying appropriate VTF it is fine, but I cant help but wonder if the lateral force also being applied makes aligning with a precision protractor a futile exercise.
How does anyone mount a non-Rega cart in a Rega arm?