I can only speak for the 2008 Prius. According to the shop manuals (4 books, about 20lb) the smart key itself has three factory pre-programmed codes. These are "burned" into the key, and cannot be changed or reset. Doors, ignition, anti-theft.

It is the CAR's computer that is "programmed" to accept the code from a key.

The key itself is not reprogrammed.

If the key is also from another 2006 Prius, I cannot see any reason it could not be programmed into your car's computer.

Except for the possiblity that your Toyota dealer is LYING to you in order to sell you a $250 blank key....