I don't think it's the IJ incremental/absolute mode that is the issue.
A mismatch between GCode assumption and the IJ incr/abs setting can cause the "wrong way loops" that people see. The default IJ mode is controlled by the General config settings. The IJ mode can also be switched within a gcode program by G90.1 (IJ abs) and G91.1 (IJ incr).
Whether coordinates, and hence movement, is incremental or absolute is independent of the IJ setting.
Absolute coordinate mode is set by G90 and incremental coordinate mode is set by G91.
Dave