I don't know the innards of the PFA circuit topology, but if the circuits are identical and the components are made to the same spec/tolerance, there should be no discernable difference. Electrons are electrons, and filters are filters; short of heat causing component drift, I don't see why they will sound any different.
Re: longer cable runs and reduced noise... that could be a function of running balanced vs. unbalanced. I thought the 5-pin binder KCY was balanced, but I can't say that I know whether or not the KCY/PFA implementation is fully balanced; if it were, then there should be no discernable difference on that front.
For what it's worth, I have zero issues running my KCYs and don't see a need or desire to run full bodies. If there is a significant difference, I'll take the convenience of active cables any day of the week, it's not like they don't make absolutely phenomenal tapes. I hear very little-to-no noise running my KCYs + PFA into my sound devices converters/preamps.