If I were you, I would call the shop that did the set up and set up an appointment with the luthier/technician just to look into the intonation. He/she should be able to show you why it can't be done if it can't or maybe with a little more careful attention will get it right. And if it can't be done, there should be some remedy available; it would just be a matter of whether or not it could be justified.
"First you master your instrument, then you master the music, then you forget about all that ... and just play"
Charlie "Bird" Parker
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