The parameter ra is defined as "Rotate by Angle: angle of rotation in degrees positive = counterclockwise, negative = clockwise". This is OK to use positive angle for counterclockwise rotation for GD extension. However, if convert is preferred through config_prefer_imagemagick, the rotation angle is passed through as '-rotate' parameter. Convert uses clockwise rotation by default which is the opposite of GD parameter of phpThumb().
So it is not possible to use both converter at the same time without patching phpThumb() or a separate rotation parameter switch.