Encuentro esta información en la página del ESTA:
If you are a citizen of the U.S., and also of a VWP country, you should not be applying for ESTA. One of the requirements of being a naturalized U.S. citizen is that you apply for, and use, a U.S. passport for your travels. While we are aware that in some cases, naturalized U.S. citizens use their alternate country's passport to travel, our expectation is that you will use the U.S. passport to travel from another country to the U.S. at both points of travel, departing the foreign country, and arriving into the U.S.
If you have a true emergency, and are unable to obtain a U.S. Passport before your travels and have only a VWP-eligible country's passport, then you will have to file with ESTA to use that passport to travel to the U.S., and you will have to use the non-resident queue when arriving at the U.S. airport using the foreign passport. Note: It is important to PRINT a copy of the document for your records. The printout is not required upon arrival into the United States, as the officers have the information electronically. Some airlines require the printout upon check-in, please check with your respective airline.
Sobre todo por lo que dice al final, deduzco que, en el mostrador de la compañía aérea en España, si la compañía es americana, enseñarle el americano (para que no me pida el ESTA), pero si no, es mejor el español (para que no mire si llevo más de 90 días en España).