Also, I'm seeing a major plot hole here.
How do you explain I-400 and I-402? The Supreme Flagship exists. The Sen-Toku class were all her direct subordinates, outside of any chain of command except hers. If they still did the same things they did in the anime, Yamato is at fault for it or at the very least needs to do some serious explaining about what those two were doing.
I would also like to note that the way they were sunk doesn't look even close to what would be needed to actually kill them. We have seen mental models survive far worse.