It may void a particular warranty claim if it can be shown that the AP contributed to the failure. If you were to have a problem with say a power window or the braking system, they would likely still honor the warranty for that.
The Cobb Tuning platform is a robust, proven system when used properly. Make sure you read and understand how to use it and you’ll enjoy dramatically better performance with little risk to your car. However, a skilled Subaru tech will be able to detect the ECU changes and any kind of drivetrain warranty claim may be denied because of it.
I find the trade off worth the risk and loaded a new map to my 2020 WRX within a week of purchase. It completely changed the character of the car and it now drives the way it should have from the factory...