Don't know about the code share issue, but I had this problem with a one way AA award ticket MNL-NRT in 2015. They wanted me to come to a ticket office in Manila in person to pay the taxes, but I was in the US. After literally hours of late-night international phone calls and over 100 emails I finally got them to except payment via phone after I emailed my and my companion's passports. Really a ridiculous process...