1 is likely to work more for social reasons, not technical reasons.  Sure, the vendor could swipe you for 0.23 BTC, if they want to leave a bad taste in your mouth.  They could also double-charge your VISA today, but by and large they don't.  Now, you do want to watch out for dishonest clerks, because they might have less of a stake and would be more interested in scamming you.  But the same way people know to do due diligence now to protect themselves from hacks of online wallets, so can people learn to avoid getting scammed by clerks (e.g. don't let the clerk snap photos of your change paper, or use method #2 or #3 whenever possible).

3, given the notes are meant to be disposable, simply crossing out the denomination and writing a new one isn't all that outrageous.  Or putting a small tear in the note to signal it has been partially spent.  Not all notes have to be printed pre-denominated.  Notice on my sample notes I simply hand-wrote 1 BTC on them and I don't consider this a terrible flaw.