Intonation methods is one of personal preference. One player’s in tune can be another’s out, so go with what sounds best to your ear.
I once talked with someone from Peterson (tuners) about the different methods people use, and that lead me to the way I have set intonation for some years now. I started usung the two octave method (in my case 5th and 17th) about 10-12 years ago. Now if I tune using just a 12th harmonic, chords just sound wrong to me. Try tuning your open note to match your fretted (not harmonic) 12th, and then your fretted 5th and 17th should be in tune as well. Compare how that sounds to you over the harmonic method.
FYI, the Peterson tech advised me to choose a method and stick with it. Trying to get two octave intonation to match 12th harmonic is damn near impossible.