Aye Dick,
You'r not trying to twist the two halves of the crank, only applying torque to one half of the crank, whilst it remains rigidly held between the crankcases.
You are applying a torque to the nut, which has forced the taper surface of the crank end and the inside taper of the alternator flywheel together. It is a friction join. The woodruff key which lies between the surfaces is nothing more than an acurate locater, it does not take any mechanical strain if the rotor is correctly installed. Hence the dynamic balancing of the flywheel, before installation, as its position on the crank is a known constant.
By using the 'BOA' on the alternator circumference and then applying the torque to the nut you are only resisting the turning of the left hand side of the crank. Providing the taper has been correctly assembled, it shouldn't move, until you apply the pulling force to the end of the crank, using the BMC Mini flywheel puller or similar.
The wheeze to ensure a good fit of the taper is to clean it scrupulously, then breath on it and bring the two halves together. The dampness of the breath creating a slight oxidisation of the two tapers, which makes them bind. If you are unlucky, a 'bright spark' will have applied a metal 'glue' i.e. 'Studlock', to the taper and then you may have to destroy the bottom end!!!!!!!!! 'Nutlock' is a different kettle of fish and I have used that to hold an abused Ducati single crank taper and alternator together and be able to seperate the two items, using a conventional puller.
As for adjusting the alignment of the whole crankshaft, with a soft metal mallet, it is indeed a delicate touch and patience in abundance that is required. However, having had to put 30 tonnes pressure onto the end of the crankpin of a Ducati single, before it would separate from the flywheel, and it being a different component part of the same assembly I think that the air wrench is unlikely to cause problems. I am happy to eat humble pie, if others with different experiences know otherwise.
My regards, Bill.