If your dealer refuses to replace your car's fuel pump after the Lexus near mishap, then just go to a different dealer. Some dealers are better for warranty service than others.
If you replace the stock tune and intake, and then remove the battery's negative cable for 15 minutes to wipe out the computer's memory before taking the car in for warranty work, then the only thing the dealer will be able to detect is that the computer's memory was reset. If they ask you what happened, just tell them that an interior light was accidently left on which ran down the battery, and it had to be disconnected for a recharge.
Of course, you'll also have to reset the time and station presets on the radio.