After hearing from Chad, the problem turns out not to be in the TGC, but in the tool's preview display, where some of the holes were being cutoff.
Even if the preview in the tool shows holes being cutoff, when the course is imported into TGC, TGC automatically expands to include all of the holes.
There isn't any need to do autopositioning in the tool, since the TGC import handles the course correctly.
I had finished the course by using the version I had manually rotated and shifted, with the edge of several holes on the edge of the editable area in TGC. I've started over, after getting Chad's feedback, and now have more area around all of the holes, nothing is being cutoff - and will reassert all of my previous changes onto the new course.
Problem solved...