At today's volunteer bike kitchen, a "customer" swapped-out driveside cottered arm of Raleigh. Upon reassembly, arms were visibly not at 180 deg. After much trial and error, a different cotter did the trick. So yes, cotters can and will effect crankarm alignment.
Customer did not want to service BB at same time...oh well, at least his arms are aligned!
Jack Romans
Sacramento, California