Amusingly, I'm seeing huge parallels between this and the whole 'Hermione can't be black' crowd, even though its very different people making up each group what they're saying is... basically the same.
Hermione in the books has no stated race/skin color or any features other than large buck teeth, very fritzy brown hair, and brown eyes. She's British, a culture which has a significant population of blacks who are considered British, and her stated features even sound black.
The story, while it deals with discrimination heavily, does not do so on the basis of real world races, and even then, Hermione herself is a discriminated against individual, so along with her features there's no reason to not think she's black or white. Black or white, it has nothing to do with who she is in the context of the story or affects the context of the story itself. It may be a story particularly about British facism, but to be in the role she plays in this context doesn't have anything to do with being white. And it's not taking a rare already role from a minority actor.
Motoko is a person with a visual and therefore clarified appearance who lives in Japan and occupies a high level government position. Japan is extremely racially homogeneous, and non-Japanese people occupying high positions of authority is not very likely due to factors alongside their rarity, especially in the context of the story, which deals intimately with the nature of the Japanese government as well as its immigration policies and xenophobia.
In this specifically Japanese story, Motoko isn't the very very rare other agent that fills that part of the narrative, but a native agent who has positions on both sides of the politics of Japanese nationalism at hand. Whites in the story, in how they're treated in that narrative's society, are solely rare agents of the current European and US regimes which occupy particular roles in the narrative, with the main story being about Japanese people trying to figure out their own sense of nationalism and how they treat other Asian migrants. The main character being Japanese actually matters in terms of how it deals with its themes and her feelings towards the migrant situation coming from that society.
One is "she can't be black" because people don't want the character they like to be black for racism reasons rather than for any narrative or thematic reasons. With Motoko, she has an essentially stated ethnicity, it's narratively and thematically important, and it's continuing the racism inherent in whitewashing leading roles in big films.
It's a false equivalency.
Edit: It's kind of like why Akira has to be set in Japan with a Japanese cast to work, since the entire premise and themes are based on particular aspects of the Japanese national identity following WW2 and their history with nuclear weapons.
You take those specific elements and its not actually Akira anymore in terms of the nuances of its themes and meaning.
And it'd take rare roles from Japanese American actors.
Edit: Plus casting Hermione as black is a transgressive move that makes a positive statement about discrimination in that industry, while making a US movie about a Japanese story where all the mains are white is the same old discriminatory crap that keeps minority actors out of lead roles. Very different situations.
You're of course free to not care until you have an arbitrary number of statements from various vetted peoples, but your equivalency there; it was nonsensical and misunderstood both works as well as how much the realities of discrimination color both sets of motivations to make them quite distinct.