JP is about the arrogant hubris of scientists and capitalists that think they can create life from nothing and control nature. In the novel genetic engineering is discussed more in depth, and the book talks a great deal about the dangers of custom tweaking life forms.
This theme is more present in the novel than in the film, but the message is there in JP1 and the point is underlined in JP3. At one point Grant dismisses the "dinosaurs" on Isla Sorna and says, "What John Hammond and InGen did at Jurassic Park is create genetically engineered theme park monsters! Nothing more and nothing less."
I think retconning the dinosaurs to have feathers would weaken this message and take away an opportunity to explore the genetic engineering angle, which I still think is very relevant discussion to be having today.
I do think it would be important for JP4 to somehow bring up the fact that we now know about feathered dinosaurs, and to explain why the dinosaurs on Isla Nubar don't have feathers.