Actually you can program used keys, but the process only works on north american delivered models. TechStream allows you to do a full smart code reset (wiping all keys) back to virgin. You can then get an unlock key for the smartbox, and re-add the "used" keys.
Unfortunately though the TechStream option to reset the smart codes fully doesnt work.
I'm even happy to pull apart the smartbox and desolder eeprom's to read / write them as required (the same way you can virginise an older IS200 ECU to accept keys) - but Lexus upped their game with the security in the IS250, so that's proving a LOT harder than with the IS200/300.
Again im sure someone knows how to do it, its just a matter of finding the right person.