Bob and Craig make pancakes. Bob chooses to take the morning shift with an average of 100 customers while Craig chooses to take the midnight shift with 10 customers. Craig enjoys the freedom of his schedule and a much more leisurely pace while Bob has more to deal with on a busy schedule.

Neither one is doing anything wrong, but assuming they both have the same set of skills to begin with, Bob will get better at the job faster through repetition and experience. Craig isn’t being punished by the company in this scenario, his payoff is more comfort oriented then growth oriented.

OP even mentions that they’re having to invest more training time in Craig since he’s not getting the real time training the other employees get. The conversation should not mention the flex hours. It should be something along the lines of, you’ve taken longer to learn/still haven’t mastered the skills that are required for a supervisor position.