Likelihood of warranty issues with an ECU tune are thin to none. It's the stealth mod of all mods.

There's no easy way to determine if a car is using the factory mapping or the kind of modified ECU map you'd be looking at. Even for a tuner staring at the paramters on a laptop, it takes a fair amount of experience to distinguish the factory map from a tuned ECU.

Intake and pulley mods are a different story. Maybe I'm paranoid, but I wouldn't put it past a tech to note an intake or pulley mod on the computer even if the car is only in for service. I've been holding off going down that road until the warranty has expired.

Did you double check the belt tension for slippage or binding after the shake-down run with the new pulley?