It only takes over a part of the UI and only when the user chooses to turn it on. On a system like Tesla with a large screen, CarPlay would be just one more panel on the screen along with others controlled by Tesla.As a manufacturer, when you give up CarPlay, you're giving up on owning the car's platform. This is fine for most car makers because quite frankly, most should have no business in developing software!
But for a car that is a computer w/ wheels, I can't see Tesla giving up control, the same way that I can't imagine an Apple Car allowing Tesla to entirely take over their GUI...