Cracks in the paint from the corner of the neck pocket are common on many bolt-on neck guitars. Stresses build up in corners and the cracks appear from there (which is why we have round windows in pressurized passenger aircraft, where we do not want cracks!). Your luthier is right, it's nothing to worry about. 99.9% of the time the crack is only in the paint, not in the wood. It is purely cosmetic and will not develop into a more serious problem.
If the glue doesn't absorb then yes, it's fine. Your luthier is the expert here, as he is the only person who has seen the guitar in person! I think you can trust him.
If you are really unhappy with this (and I understand) you should talk to the person you bought the guitar from. Otherwise, enjoy your wonderful guitar!