"I would not rely on the PHD2 algorithm for most AP mounts. It will not be able to accurately predict any residual periodic error that could already be taken out by AP's PEC mechanism. It may be useful if there is periodic error not correctable by PEC because it doesn't repeat in phase every worm cycle, but there are very few cases where that might happen. "
Did you mean PPEC algorithm? There is no PHD2 algorithm in PHD2.
My intent was not to 'hype' PPEC, but to answer the OP's original question about PEC and guiding. I extracted info from the PHD2 Help that discusses that question and it happens to fall in the PPEC portion of the manual.