nope - each flight outbound and inbound are treated separately. If the outbound flight is out of EU country that flight is covered. the inbound flight isn't as it starts in a non EU country and is operated by a non-EU airline.
so when you fly MUC-IST-HKG / HKG-IST-MUC only MUC-IST-HKG is covered by the EU.

Every online-service helping passengers to get their compensation will deny to process HKG-IST-MUC claims on a non-EU carrier.

Turkey has very similar passenger rights - if something happens on the MUC-IST-HKG flight you will get compensation according to the Turkish passenger rights - the amounts paid out are identical to EU261.