Thank you for playing the game! I wasn’t expecting many people to score 100% completion. :D
The three dots thing is there to keep some things cryptic on purpose, so there is some exploration and experimentation left for the player. It’s usually possible to finish most of the levels without a full understanding but the combined puzzles (the ones that unlock the bonus levels) require ~full understanding of everything. This is a bonus (optional) content, so I felt that it was fair to keep it challenging. :)