You could probably fit the moon logic and one-pixel-clickables into an optional hard difficulty setting -- introducing a few additional puzzles that only come up for people who are actively going for the Full Experience. Maybe one of the keycards is broken, so you have to glue the two pieces together with partially-chewed gum that's stuck to the bottom of one of the magboots, or the chemical recipe is found only in a PDF manual as copy-protection, or ....