While looking into this a bit further, I ran into a thread on a mailing list from 10 years ago, which brings up an interesting point:
http://astro.umsystem.edu/apml/ARCHI.../msg00523.html
Do modern mounts over-ride PEC when receiving guiding input, or do they use it to augment PEC replay? If the behaviour has not changed, PEC may well still be mooted when autoguiding.
On a side note, I once bought a scope from a man who thought he had to program his PEC every night. Yes, he sat there for 30 minutes every time he went out, manually training & checking his PEC. I think he was a masochist.