Like when a tuner copies/pastes the Base Timing table into the Advance table and then does a WOT pull?
^ This ^
If you datalog / monitor the tune to make sure things are in line and you keep up with your maintenance, your car shouldn't have an issue with Cobb S1/S2 tune that wouldn't have happened on a stock car. The fact that there is aftermarket calibration on the car will lead to a warranty claim denial, but that's the price you pay to have a car that is faster and drives better. If you want the peace of mind to know your warranty coverage is in place, keep the car stock. If you choose to modify the car and there's a powertrain issue, well, pay to have it repaired, because you broke the contract between you and Subaru when you upped the output of the engine (they promised to cover the product with their specifications).
In regards to leasing, there may be a clause that prohibits modifications in your contract with your financial institution. Make sure you read that contract before you make any decisions.