Peter, after digging out my manual, I think we're both right but I wasn't very clear.
Some Petersons offer a proprietary temperament called GTR (and a similar one called BAS), to be used with standard tunings, nuts, and intonation procedures, that improves the 4th and 5th intervals and makes a sweeter sound when fretting chords. In this case they tell you to set intonation using EQUal temperament, then tune using GTR.
They also have separate sections about setting intonation, and tuning, when using either the BF or Earvana systems. In these cases, it is indeed a package deal as you say.
Lots of interesting stuff here. I also re-read the section on setting intonation (without special nuts or anything), in which they suggest an alternative to the usual compare the 12th fret note and harmonic - you instead adjust the bridge saddles until the notes (not harmonics) at the 5th and 17th frets are both in tune.
As fascinating as this stuff is, it just makes me happier all the time to not have frets...