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I think Flick's punishment was more severe. It doesn't give a financial punishment but he can't find time in the match that week. Just think, your most important weapon doesn't come to training and Flick doesn't let him play in the match in order not to break discipline. This is a big threat to the other players. I'm sure everyone comes to training on time.
Each coach has his own rules for handling and increasing the discipline of the players. The punishment can be in the form of money and other things, but to be honest I don't know exactly how Hansi Flick maintains discipline among the players. If what you say is true, then I really think every player will obey it and will not violate it. However, such punishment will also have an impact on the team, especially if the coach has to bench a main player due to disciplinary problems.
But whatever punishment the coach takes to increase discipline, it is the best for each player. Basically it is a natural thing because small things like that can have a big impact on the quality of the game and also on the players themselves.