It's true that data is often written out in a logical order, but like you say, that's only because the program that created it was designed that way. I've definitely seen PDF files where tabular data is almost in a logical order but every now and then cells have been jumbled around.

But what I've definitely seen is documents where the characters are deliberately jumbled up and a custom font so that visually everything looks fine. I know this, because there was one specific case where I wanted to extract about 5000 words in a vocabulary list and it was hard to decipher. They'd used several such fonts in the single document as well, so there wasn't a one-to-one mapping of the text encryption. They'd also put a watermark under the list, so you also couldn't easily do OCR of the final screen image either.