The last CP-2000 I saw said "It is not necessary to file an amended return (Form 1040X) if you don't agree with our changes.  We'll review your response and make any applicable corrections.  However, if you choose to file an amended return, write 'CP2000' on top of it and attach it behind your complete Response form."  (Bold face in original.)   

The problem these days is that people want to file the 1040X electronically, and it ends up somewhere like Ogden, while the CP-2000 is being worked somewhere like Kansas City.  The 1040-X is designed for IRS clerks to do data entry, not for IRS examiners to figure out what happened.  If you want to tell your mother you love her, don't send her a form with three columns to explain how much.  Use the English language she (probably) taught you.