turbine shaft alignment.

Silly question:

When the alignement is initially done, it is under ambient "cold conditions". In this environment, has the thermal expansion been factored into such that the turbine is actually out of alignment at ambient conditions but "grows" into aligment at the operating temperature?

Correct. Reassemble completely. If it was a steam turbine you would engage the turning gear and check again and then go through you warming up procedure monitoring all the time.