Replacing characters with identical-looking unicode chars, adding extra spaces here and there, adding newlines (and more spaces :)), adding random typos, use dictionary with "safe" word/phrase replacements etc. And don't forget about formulas, charts etc - pure text version is not too useful on its own
If you deal with fiction and the like where you basically have just text then I think that's correct: it would be trivial to detect the watermarks in various copies by simply comparing them. I was dealing with PDFs containing tables, formulas, illustrations, etc., so a plain-text version would be unusable.
Randomly choose 3 big paragraphs in the entire ebook to add an extra newline in the middle of at the end of a random sentence. This would be my choice if I had to do some kind of invisible watermarking, at least.