Aligning cart on Rega style arms without defeatable anti-skating?

If I understand you correctly, the simple answer is yes, it can be a pain in the butt to set up a cartridge with antiskate applied. All tonearms that I have ever used permit disconnecting the antiskate device while doing an alignment. Have you actually demonstrated that there still is a residual anti-skate force, even when you are set to zero?

Not intending to insult, but make sure your table is totally level when aligning your cart.  Sometimes non-level tables can mimic antiskating/skating forces.  This is easy to demonstrate when using a Wally Skater.

Of course the first thing I did was to level the turntable, then zero out the counterweight and anti-skate to attempt to balance the tonearm.  When doing this it is obvious to see that the anti-skate was still somewhat active since the arm will slowly swing back to its rest. 

Just wondering if other Rega owners are experiencing the same thing, and whether this force is enough to deflect suspension any meaningful amount when trying to align to a protractor.

Some protractors have a tiny dimple in the surface at the point where you want the stylus tip to sit.  Catching the stylus in the dimple is typically enough detention to immobilize the arm while you are trying to do alignment, even with a bit of AS in play.

I am considering getting such a protractor but the issue isn't so much as to get the cartridge to land on the right spot of the protractor, but whether the anti-skate force pulling on the cantilever would cause it to sit askew and not "square" to the body once it is on the grid alignment point.

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.