You won't clear customs in MUC (unless your baggage is only checked through to here - in that case you just exit the baggage area and out into the main arrivals area). Like I said if your bag is checked straight through to FCO then you will clear customs there. Depends on your companies interline agreements with baggage transfer.

Rgds and happy flying.

ps: If you mean immigration i.e. passport control then yes this will be checked at MUC regardless if you are transferring or not. But as you mentioned customs I assume your question relates to baggage clearance.