I compare the 12th fretted note to the open. When they both are in tune, my bass is always intonated. I test this by comparing fretted notes and their octaves all the way up and down the fretboard.
I've never used harmonics, and always had near-perfectly intonated basses and guitars using this method.
"That's right Mr. Martini, there is an Easter Bunny!"
WANTED: Vintage Hagstrom Concord in RED