The customs clearance in the satellite is for transfer passengers. When you enter the EU at MUC with an onward flight (e.g. to BER) you clear customs for handluggage at MUC and customs for you checked luggage at the final destination (e.g. BER).

Thanks for the informative post! Out of interest, if your final destination is Munich are you directed to go through passport control in the satellite terminal, or did you just decide to do this? Did you follow the signs for exit/baggage?