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One thing I've found that helps with intonation is checking at the 19th fret for both the harmonic and the fretted note. I've had folks use electronic tuners and a few other ways and the 19th fret always seems to be most accurate. Plus you just drop back to the 17th fret for the 5th string which is the equivalent of the 12th fret for the other strings. It never hurts to check both at the 12th and the 19th on the other 4 strings.
My fretboard is scooped for frailing, so I only have 15 full frets and two half-frets. The highest I can go is the 17th fret.