Well, of course the dealer is against it, however Magnuson is actually the company that designed and built the superchargers for use under the TRD name on the first and second gen Tacomas and the current 5.7L Tundra. They were sold at Toyota dealerships and held a complete factory warranty. So I would gander that Magnuson knows a thing or two about maintaining reliability for longevity. Many of those supercharged trucks are still running around at over 200k miles with minimal maintenance and issues.
Sure the charger will of course put a bit more stress and wear on the motor and drivetrain, but I am willing to guess it is not enough to really make much of a difference in the longevity of the truck. No one knows for sure obviously as the 3rd Gen has the new 3.5 L motor, but I myself am pretty confident. Toyota makes a pretty stout product that I expect to live a long life and the Magnuson charger is running a low enough boost and modest gains that I don't believe it is seriously stressing the motor much.