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setting intonation on fretless bass question

I know how to set intonation on my fretted basses but have never done it on a fretless. I have a peterson strobe tuner and I'd like to do a setup on a new fretless bass I just got. Any help would be appreciated. And yes, I did a search but pretty much everything I found was about fretless playing intonation, not the initial setup.
 
I set up my fretless like I do my fretted.

Play harmonic at 12 "fret" (yeah, no frets on a fretless but you get the idea), compare with pitch of depressed string (at same place, harmonic at 12th "fret" and note of 12th "fret" should be the same notes, but different octaves.) Adjust bridge saddles as necessary, rinse and repeat until intonation is set up properly.

The rest you have to do by ear, obviously - in that way, fretless is a bit more forgiving when it comes to intonation setup, you can always adjust by ear...
 
If it's unlined, figure out the scale length...... measure 1/2 of that, from the nut, put down a piece of painter's tape (edged up to the 12th position), use a credit card, to hold the string down to that position and compare the differences between your tuned open note and the 12th position........there it is.
 
I set up my fretless like I do my fretted.

Play harmonic at 12 "fret" (yeah, no frets on a fretless but you get the idea), compare with pitch of depressed string (at same place, harmonic at 12th "fret" and note of 12th "fret" should be the same notes, but different octaves.)

No. They should be the SAME octave.