Oddly, I also have a similar question.

So, if my passport expires in three months or less (say in one month) but I am only transiting in FRA or MUC on my way back to my home country (e.g. US to Japan via FRA or MUC), would Germany authorities allow me to transit in FRA or MUC?

Based on what I read in the rules (provided by oliver2002), I should be allowed to transit despite the fact that the passport expires in less than 3 months (I think the rule is 6 months).