Consider the infinitesimal benefit of storing config data in flash. Now consider the cost of adding flash capability to a performance logic process. Intel doesn't even want the trouble of thick oxide devices for I/Os in its MPU processes. Flash? forget about it.
Sorry to break the news to you but that is how it's done. I probably can't go into the specifics as they are proprietary but a lot of information is programmable and stored on the device.
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