You're basically talking about exceptions, especially in James Gunn's and Taika Waititi's case. Personally, I didn't feel much of Ryan Coogler's influence in "Black Panther."
Anyway, oftentimes Marvel Studios' graphic team has already put together the entire visual style for the movie, from costumes to gadgets and environments, and even completed pre-viz for the action and effects scenes --- and that's BEFORE A SINGLE DIRECTOR IS EVEN BEING CONSIDERED.
Marvel Studios has never been the most director-friendly studio, and that's a fact. That doesn't mean that a peaceful collaboration isn't possible, but that their movies have to fit a certain style, feel and criteria. The franchise is handled like a TV series, where the showrunner (Kevin Feige) has the final word and shapes the movies, but guest directors come in and do their job to add another episodes. And sometimes there's also some space for a little experimentation.
A better example of hiring great directors and have them fullfill their vision would be Tim Burton and Christopher Nolan on the Batman movies, Sam Raimi on his first two Spider-Man movies, etc. That's where you really feel that the studio hired a talented filmmaker, and let him put his stamp on these iconic characters.