You rotate the BLDC motor in order that it will generate a AC wave form on the 3 phases.
Both the A phase and the corresponding commutation pulse is monitored on a scope and the encoder turned until the commutation is as is shown on the PDF.
IOW you check one phase at a time.
AFAIK the Yaskawa AC servo is just that AC so the BLDC version may not apply as far as alignment .
Al.