You and Fender are both right. A slight twist doesn’t really affect the playability and a lot of Fender necks have this issue. Many players don’t even know their neck is like this. But you are also right to say that an expensive Custom Shop guitar should not have any twist issues like this. Part of the problem is that you should have seen this twist before you purchased such a guitar. Even though it should not be your responsibility ultimately it is, because most guitar store guys would be ignorant to this and probably try and tell you that you are wrong to avoid any accountability. I’m sure this twist was in the neck before you purchased it. This is not an issue that miraculously appears out of nowhere. The guitar made it past Fenders QC and where ever you bought it passed their QC which puts it on you, which is unfortunate. If you have had the guitar less than 90 days, I would return it for a refund and buy something else. If not, you could press Fender and try and get them to replace the neck? Don’t give up in this because the squeaky wheel gets the grease. I’d call them every day until they resolve it for you, eventually that will, I think? In the worst case scenario you could buy a replacement neck the resell the original neck, but that would suck.