While there is no denying that Welles's contract was unusual, especially in the way it said that Welles was to have four responsibilities (actor, writer, producer and director) and a right to final cut. But disregarding the comparatively unimportant part of him also acting, this was not unique or unprecedented. Consider for example F.W. Murnau's contract with Fox for making Sunrise (1927), which gave him almost unlimited freedom (for his next two films for Fox that freedom was severely curtailed), or Ernst Lubitsch's contract with Warner Bros. in the early 1920s. ("Lubitsch shall have the sole, complete and absolute charge of the production of each such photoplay /.../ there shall be no interference of any kind whatsoever from any source, with Lubitsch, with respect to any matter or thing connected with the production, cutting and final completion of such photoplays.") That shows the high esteem in which the two Germans were held but it was not just already established directors from abroad who could get good deals in Hollywood. Consider Preston Sturges at Paramount for example, or Frank Capra at Columbia, and many other directors including some that are more or less forgotten today. Mitchell Leisen said once that since he was a "top director at Paramount" he just "snapped" his fingers and got whatever he wanted. (I wonder how accurate that was though.)
But the contract itself is not all that matters. For two case-studies let's look at two films from 1938, the year before Welles signed with RKO, at the height of the power of the studio system and at two different studies: Bringing Up Baby, made by Howard Hawks for RKO, and Jezebel, made by William Wyler for Warner Bros.
Hawks had signed a deal with RKO to make up to three films. After much time was spent on coming up with ideas and concepts Hawks settled on a short story by Hagar Wilde he had read, and called in Dudley Nichols to help make it into a feature-length script, gathered a cast and began filming. In Wyler's case, Warner Bros. already had Jezebel in mind for a film, and Wyler had many years earlier spoken about wanting to make it, so he was hired for this one film.
Once the contracts were signed Hawks and Wyler were in charge. They made all decisions, got the writers they wanted, went way over budget and over schedule, yet the studios could do nothing. The two films were made on Hawks and Wyler's terms and on their own schedules. They were responsible for the shape and form of the scripts too, and called for help with it from those they felt were right for it, in Hawks's case Nichols and in Wyler's case John Huston. (Wyler did on several occasions sign Huston up for writing or polishing scripts.) All the studios could do was hope for the best and write exasperated memos, such as one at RKO which complained that "All the directors in Hollywood are developing producer-director complexes and Hawks is going to be particularly difficult."
You could argue that Warner Bros. had been expecting to get a Warner Bros. film but instead they got a William Wyler film. But they had reason to be pleased with the finished result though, as Jezebel was a huge hit whereas Bringing Up Baby was not. RKO did not have any particular film in mind when the contract was signed but were still disappointed that they got a Howard Hawks production. Despite Hawks's deal for potentially three films only this one was made and then RKO had had enough of him.
The following year, 1939, Hawks made a film for Columbia and Wyler returned to his old partnership with Sam Goldwyn. Now though Hawks was more fortunate than Wyler, as he made Only Angels Have Wings without interference, a film that is not only one of his best but also what might be called the purest expression of all his themes and then current style. Wyler on the other hand made Wuthering Heights, where he and Goldwyn had different ideas of how it should end. Wyler's version was final and tragic, an image of Heathcliff frozen to death in the snow (the film is not a particularly faithful adaptation). That was not something Goldwyn could stomach and as Wyler refused to do a new ending Goldwyn had H.C. Potter direct a brief coda to lighten the mood, and removed Wyler's last scene.
The point is not that Hawks, Welles, Wyler, Murnau, Lubitsch were unique but that quite a few filmmakers in Hollywood could make films with great creative freedom, and not necessarily with less of it than their peers among prestigious European and Japanese filmmakers. Another point is that one must differentiate between staff directors and freelancers. A third, central, point is that the actual, lived reality in which they and all other filmmakers work is complex, constantly changing from time to time, from film to film, and often unsuitable for general theories and generalisations. It is this complexity which makes studying film history so interesting and exciting.
Charles Vidor directed a couple of re-takes with Rita Hayworth for Only Angels Have Wings. I am not sure why, but in any event it does not effect the film.
Some sources and references:
Thomas Schatz's book The Genius of the System (1989)
Scott Eyman's book Ernst Lubitsch: Laughter in Paradise (1993)
Jan Herman's book A Talent for Trouble: The Life of Hollywood's Most Acclaimed Director, William Wyler (1995)
Todd McCarthy's book Howard Hawks - The Grey Fox of Hollywood (1997)
Vanda Krefft's book The Man Who Made the Movies: The Meteoric Rise and Tragic Fall of William Fox (2017)
Richard B. Jewell's article "How Howard Hawks Brought Baby Up: An Apologia for the Studio System" (1984)
Mitchell Leisen was interviewed by Leonard Maltin in 1970 but now I do not recall for which publication.
Speaking of lesser known filmmakers, I am curious about the contracts of someone like Mervyn LeRoy, perhaps the most successful and powerful person among the staff directors at Warner Bros. in the 1930s. Further research is definitely warranted, not just because he made such important and fine films as Little Caesar (1930), I Was a Fugitive from a Chain Gang (1932) or They Won't Forget (1937) but also because he and producers Hal B. Wallis and Darryl F. Zanuck can be said to have been particularly important in the creation of Warner Bros. particular style of filmmaking. And how did he compare to someone like Roy Del Ruth, even lesser known today yet Warner's highest paid director at the time? But having read whatever books and articles about LeRoy I could find (which was not much) I was not particularly more enlightened, other than that James Cagney was not at all a fan of him as a director or as a person.