I absolutely agree. This trope is being invoked for half of the afro-american characters who are noticeably clever, helpful or otherwise impressive. To take up your example: Morgan Freeman in the Batman Begins movies is highly intelligent, helpful and an employee of Bruce Wayne, which or course makes Wayne his "master" (insert head-desking here). But pretty much everyone in that movie is very exceptional. Scarecrow is super-intelligent and mixes up a "magical" poison which causes character-specific hallucinations. Clearly a hint towards voodoo! Magical negro! Oh wait, wrong ethnicity. But there's this magical mentor full of ancient wisdom showing confused Bruce Wayne a path and basically starting his career as Batman! Magical neg... oh wait, no. The butler! He even calls Bruce Wayne "master"! No, foiled again.

The trope page looks as if every really impressive, cool afro-american character immediately gets classified as this. What does that leave? Afro-americans can be either delivery men or other minor characters (which is of course racist) or scientists, fighters, good friends, which is racist too because it's this trope?

You're not getting it. The "Mystical Negro" trope doesn't apply when a highly skilled or talented Black character does anything at all that helps a white character improve his performance or be a better person. The "Mystical Negro" (1) really does have supernatural powers OR superhuman levels of humility, patience, and generosity, but he focuses them on helping the white main character only, and (2) often does so to his own detriment (up to and including his own death). The main question that he raises in your mind is "If he could do all of this, why didn't he help himself, or help other black people deal with Jim Crow/slavery/racism?!" So Morgan Freeman's character in the "Batman Begins" series doesn't fit this mold at all, nor would a black Gandalf. Who does? Bagger Vance. John Coffey ("The Green Mile"). Noah Cullen ("The Defiant Ones"). Dick Hallorann in The Shining (the book, not the movie). The list goes on. But the people you've named aren't on it, nor is this trope meant to somehow demean talented or skilled Black characters. Somehow you've gotten it twisted.