The commercial sense in that is that the airline sells tickets that can be modified and cheaper tickets that can not be modified. There is also a MCT, which means that this minimum transfer time allows for smooth connections for most of the passengers under normal circumstances. If the MCT is respected and there are no extraordinary conditions, the ticket conditions apply, which means that the airline can change the ticket, but at a fee. Which is exactly what happened.

Customer bought a ticket, feels uncomfortable with the ticket afterwards and expects the airline to change it free of charge... it does not work like that in Europe. It is less customer friendly than for example in the US, but there is a commercial reasoning behind it. The airline offers a cheaper ticket that is restricted, if they don't enforce the restrictions, customers would not buy flexible tickets any more. In the end, the airline thinks it is more interesting to enforce ticket restrictions than to lift them to keep a customer happy.

I also totally understand the frustration of OP, and indeed LH messed up, but honestly they could not know the aircraft would be stuck in MUC witt ATC restrictions...

I however have no understanding for the drama, the judging, blaming, contacting LH to ask them to fire the employee, stating nonsense about compensation, ask other users not to comment simply because they don't agree, and so on.