Hmmmm....I would try to fight it. Do you have a lawyer that could look at it? It seems that the city should not be enforcing a more restrictive code that they, in theory, have no control over....
I don't think I need to go that far. I have a detailed email thread with the Community Construction Manager where she explains the larger setback is for the main structure whereas the patio (whether attached or not) is an accessory structure and should only be held to the standard setback. She has actually been quite a pleasure to work with and very prompt in her responses

This is the 6th time this corner lot setback has ended up biting me and 2nd time on houses I've owned

Here's the detail:

Have you looked into getting a variance? Referred to in our city (Clovis) as a "minor deviation." There is CA state law that provides for this. You just have to make a factual showing of these four or five different criteria. For us, we had a lot coverage issue, and on the application I was able to adequately give them a factual basis for the criteria with a little creative thinking. Building department should have a form application.
This will be my next plan of action. I hate to take things this far and usually when you do they end up throwing up a bunch of other hurdles that you have to jump through.
I have a pretty strong case (at least in my eyes) so I'm really hoping I don't need to pursue a variance.