Maybe it’s written in “pure Java” in the sense that the Minecraft source code is all Java. (Maybe. I don’t know.) However, it definitely has dependencies that

Maybe it’s written in “pure Java” in the sense that the Minecraft source code is all Java. (Maybe. I don’t know.) However, it definitely has dependencies that are not pure Java. I think Minecraft used to use LWJGL, I’m not sure if Minecraft does use it any more, but I wouldn’t be surprised if LWJGL or other libraries dropped 64-bit platform support for various reasons. Inside LWJGL there’s use of JNI.