Once the course is fretted the strings may not sound exactly at the same pitch anyway, depending on intonation, deliberate or indeliberate bending, and the difference between the octave string of one course and the fretted note of another (eg, octave G string and first string third fret). Though my own 12 string suffers little of the tuning troubles about which some complain, and I tune the open strings exactly, and then check the octaves between fretted and unfretted strings and tweak as and if necessary, some "chorusing happens anyway. That slight chorusing effect of out of tune strings should be slight (be careful it usually gets worse up the neck or capoed), so I let the inexactitude of the tuner, operator, and intonation look after it for me.

In other words, I deliberately tune as close to pitch as possible and let the guitar do its 12 stringness, which it does beautifully.

Peace, Mooh.