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The "clone" keys sold by Walmart and the other big box stores are indeed programmed but they are the exception. They're considered to be "one-time programmable". "Regular" PATS keys are not, they're pre-programmed with a unique RFID code that is then programmed into the vehicle's system. .....
Sorry, it's the software engineer coming out in me.
The code loaded into a key is data, not software, but is commonly considered being "programmed".
An original PATs key probably has a factory installed ROM chip.
A clone key would have a write-once-read-many chip.
The data is read from the chips and stored in the vehicle's memory of saved codes.