Depending on your airline, there is something called Rail & Fly available, which gives you a coupon for any long distance train to anywhere in Germany on your day of arrival. That would solve your risk due to a late flight arrival.
Without getting Rail&Fly, I would agree with SLA, go regional with a Bayern-Ticket or the Deutschlandticket.
However, I would not use the 1:46 connection SLA suggested. To get that 1:46 train, you have to take the S-Bahn 41 minutes into the Hbf and wait 18 minutes for the train, so add an hour to the whole trip (2:45), MUC to Nürnberg.
I would consider taking the 635 bus, 18 min, to the Freising Bhf and catch the RE50 from Freising to Nürnberg. You can purchase the Bayern-Ticket on the bus. But, you'll only have 3 minutes in Freising to catch the train to Nürnberg, so you'd better know where you are going.
Where are you coming from. Unless you are importing items for resale, which have to be declared, you don't have to go through customs. But if you are coming from outside Schengen, you will have to go through immigration (passport check).
BTW, the 10€ penalty with voucher only applies if you cancel the ticket before the 1st the day of validity. If you arrive late in MUC, it's too late then to get the voucher. You lose the full fare.