I don't think this is unique to (or attributable to) scarf joints.
The truss rod on a guitar neck only dials in the desired amount of bow from about the third fret up. If your neck develops a slight backbow in the lower register, loosening the truss rod won't do anything but make your action really inconsistent from one end of the neck to another.
In some cases, you can compensate for it by doing a crown & polish on the frets, and a bit of tweaking of the nut height, if necessary. If it's really bad, you might have to yank the frets and have your fretboard planed to get it true again.