If we agree that the referee has the right to authorise modifications to the pitch markings (which I think he does), then yes, at that point they can do what they like to the penalty mark until the ref tells them to stop.
And if you're sitting down and taking a LOTG exam, the answer has to be a caution.
I disagree that the law includes the concept of "oh, well you would have given permission anyway". All of the actions I list and the actions you list are illegal for a player to just do. If asked for permission, a referee might allow some of them to happen and (you would hope) would say no to others. But the distinction between those actions only applied once permission is asked for and granted - in the absence of a question and an affirmative answer, we've come up with a list between us of sanction-able actions.
So in your example as well, the correct answer in law would be to show the yellow. The choice to apply law 18/spirit of the game is yours, but that doesn't change the fact that your answer isn't technically supported by the LOTG.