Microcode is stored in a ROM (usually programmed by the presence/absence of vias or contacts), and patches are stored on the motherboard and loaded at boot time into an SRAM on the processor (which is always lost on poweroff and may be lost on reset depending on the specific implementation). There are patents that disclose a LOT of detail if you're interested. The ROM won't meaningfully degrade; if the motherboard flash degrades, well, you can't boot anyway.
As for differentiating products made from the same piece of silicon, I believe that's usually done by blowing fuses (basically vaporizing or otherwise damaging a small wire/conductor, by running a high current through it).