Ok, I missed the part about only being a factory retune. THAT I can see them doing, and preserving the warranty, since they technically still have full control of all performance parameters. I thought someone was saying they would still warranty the car within a certain range of mods and tune for a lump sum.
As far as the manufacturer going after all the performance mod money that has been left on the table for the after market, I've never understood why they hadn't done this before. They can scoop a lot of that money by offering it through a factory option program.