My dealer, Lexus of Dayton, sells their certified cars with 2 master keys. They said it was part of the certification. In fact, one of my master keys was missing and they ordered another for us at no charge. Maybe it's just part of their certification. They have been great.
They are also the number one rated Lexus dealer in the nation. Maybe this is part of the reason for that.
Also, Lexus of Dayton is opening (in the next month or two) a second local dealership dedicated to Pre-Owned vehicles. It is the first one of its kind in the country. It will have its own service department and parts department. All other dealerships are combined.