Author here, happy to answer questions about any part of this. The scoring weights are hand-tuned from playtesting, not learned from data. Would love to hear from anyone with psychometrics or spatial cognition experience.
You are definitely correct, and that is how I am solving all the puzzles as well. However, I've encountered many people that couldn't wrap their head around even the mirror across the fold line logic. For such people, the techniques I described help to come up with puzzles that feel "hard" for them. Thanks for giving it a try.
In reverse order of the folds, just mirror all holes across the fold line.
https://icfpc2016.blogspot.com/2016/08/pdf-for-task-descript...