It's important to realize that to play in tune on a fretless you have to adjust your finger placement depending on which part of the neck you'r playing. It's common for people to set fretless intonation so that a note is in tune when the line is directly in the middle of the finger. If this is done for the 12th fret, it forces you to play very sharp (past the line) in the lower registers.
If you set it like this for the 12th fret:
You might have to play like this in the 1st few frets:
Setting the intonation with the finger slightly behind the 12th fret gets these results:
