Well, let's think about it. The open string and the harmonic at the 12th fret (or very close to it - read on) will ALWAYS sound the same. The "12th fret harmonic" is simply the mid-point of the string length, so what you are checking is the open string against half of the open string !!!

Intonation is setting the lengths of the strings so that they LINE UP accurately with the frets. In order to accomplish this, a reference to the FRETS must be made.
So to set intonation, you compare the 12th fret fretted note to either 1)the open string or 2)the 12th fret harmonic. Usually, the 12th fret harmonic is used. When these agree, then your intonation is set.