Secondly, what does Intamin have to do with CP modifying an existing ride?
I don't know for sure, but it sounds like it's between any warranties that still exist on the ride including the ride control systems, any sort of negative press they may receive if the park isn't clear on who did the renovation, and possibly an overall bad relationship where the manufacturer is losing sales of new products or parts to the park/corporate.
The thing with cars is that people go back to the dealer all the time for performance upgrades - anything between tune-ups to replacing engine or drivetrains. Then there's also lots of third party shops for this work too. But in either case, most people bring their car in and few people are inconvenienced in the process - a coaster has far fewer choices for who outside the trained park staff works on it, and those folks have to travel to the ride. So it's far more noticeable anything's happening, and both the park and the manufacturer potentially have their reputations on the line when it does.