Normally I'm pretty open to the idea that something has dogwhistles. I saw someone post about your blog negatively and was ready to side with you over it, but looking at your actual blogpost, I feel like you're just seeing what you want to see.
To be fair, I'll agree with you on the black-coded villain - that sort of villain design that evokes black people is a staple of the era the anime is trying to emulate and carrying that racism forward into the modern day is not a good look.
Everything else you point out, though, seems like a huge reach. For example, "children are the future" is a pretty common sentiment, and there's a reason references to the fourteen words need to stick to a pretty specific sentence structure to be understood as such. Similarly, the idea that a reference to Amaterasu is code for antisemitism because of the connection to historical to race science ignores the many many other cultural connotations Japanese viewers will have about their country's creation mythology. Would you think the same about a reference in western media to Zeus just because white nationalists always evoke Greek and Roman mythology?
Anime has a lot of problems - racism, sexism, queerphobia, apologia for war crimes, you name it - in the fandoms, in the creative staff, in the works themselves sometimes. But this really isn't the Nazi-coded anime you seem to think it is.
Oof, that episode was a LOT. The writing, direction, and animation are all on-point, but this is going to be tough to get through. Takopi's upbeat, cartoony reactions to real, serious problems were painful to watch, but I think it's only going to get worse as he learns more and more what kind of suffering exists in this world. I definitely want to keep watching this, but I'm going to need to make emotional space for it, because jeez.