I wouldn't want to be the one with my neck on the line in court over this.
Consider that .torrent files also don't have the content, yet torrent sites which serve them and provide tracking for torrent clients are having to play cat and mouse with copyright holders.
That said, so much of what we knew about copyright and software in the 90s has been overturned by subsequent rulings or even statutes (like the DMCA) that if you wish to avoid being burned by copyright suits, you must retain an attorney knowledgeable in this area of law. (Which is true in any case.) As an example, look-and-feel copyrights are back on the table thanks to The Tetris Company LLC.
These instructions do not increase the number of people who have copies of the work, and so no copying is taking place; copyright should not be applicable here. The licensor may argue that license clauses is being violated, but not copyright; i.e. the users are using the software in ways that they don't like (use is not copying or redistribution).
(Assume for this question that the Mona Lisa was currently protected by U.S. copyright.)
To the extent that it's "based on" copyrightable expression in the Mona Lisa, yes. AIUI the key question is: would a viewer recognise the Mona Lisa from your transparency? And that would be a question of fact for the jury; personally guessing I'd say probably not from just the position of a mustache in a frame, probably yes if you included e.g. an outline of the pose. (In which case it might still be protected fair use, but it would be a derivative work, and you'd have to make that positive defence).