Only the security charge is connected to your length of stay (ie if you are really going thru security). LH shows the follwoing during purchase of tickety.
The German Aviation Security Charge is refundable if you are a transfer passenger arriving from the USA, Canada or Montenegro in Frankfurt without undergoing an additional security check by the Federal Police. For refund of this fee please contact the Service center
The German passenger service charge is the cost of the airport translated onto your ticketed destination and calculated taking into account if you are just in transit or breaking your trip.