I suspect once the initial setup and breakin is done, you're ok to switch boats as long as the motor is propped to the recomended rpm, and the setup is done per factory specs.
He just needs to run it up to power to make sure everything is good. The easiest way to do that is to hook it up to the boat. That gives him the opportunity to make sure the boat's wiring and cables interface properly and the motor performs well. He's willing to throw in the installation to reduce the chance you'll have to bring it back with a concern later.
Switching it yourself won't void the warranty, you just lose the benefits of having the dealer check things out and making sure you're good to go. If you're confident in your abilities there should be no problem. If there's anything your not sure about, ask if you can bring it in to be checked over once you install it. I'd expect to pay a few bucks for this service, but it may be worth it for peace of mind.