if only one flight coupon has to be issued, that the direct miles will apply.
Mileage calculations vary between different ticket issuing airlines. UA 'applies' airport to airport miles (Different New York airports: EWR, LGA, JFK will show different mileage calculations when booking with UA) - LH applies airport-city to airport-city miles (example: LH FRA-EWR and FRA-JFK show the same mileage with LH)