A possibly explanation of different estimates is that they can replace arms singly or in pairs and for warranty claims they will probably try to replace only one, for cost reasons.
For the front upper control arms you should check they are using the new redesigned parts (128832x) because they should last a lot longer and then they have to replace both at the same time. If they use the older part number they can get away with just replacing one side.
IMO it's worth paying for them to both be replaced with the new part. In the UK the total job costs around £200. I can't see where they get $668 from so maybe you can show us your estimate?