I had a similar issue last year with my passport being valid less than 6 months at the time of entry to Germany, so I wrote to the German consulate in my home country. The reply I got was "The passport must be valid for at least 3 months from the expected date of departure from the Schengen countries, including Germany." (bold for emphasis)
Flying to the country of issuance of your passport, naturally, is not an issue even if the validity is less than 6 months on the day of departure - because you're simply a citizen returning home.