In the end the prompt just says “Do you want to go to the page you’ve left off or to the first page”. “Start over” isn’t the default text for the “Cancel”-Button 😉 It should be much easier to reset the variables this way manually than preventing the course from resetting them automatically in case you didn’t want to start over.
With regards to the LMS I know (moodle): The bookmark is meant to enable a user to continue a running attempt, i.e. to go on with the variable values already achieved. To start over I’d make moodle start a new attempt with all variables in their default values. Resetting the current attempt is not really something the LMS means you to do.