I think the answer is that it's arranged that way because that arrangement makes it easier for humans to interpret. Because humans prefer to see data in such 2D arrangements, file formats like PDF were developed so that 2D layouts could be defined and preserved across platforms.
Hence the fundamental problem here is that we want computers to be able to read data that is designed for human readability. That is not an easy problem and it is in fact a large part of what people mean when they talk about "AI".